**From:** James Starlight (*jmsstarlight_at_gmail.com*)

**Date:** Tue Sep 10 2013 - 11:29:17 CDT

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Thanks again for suggestions!

That problem has been solved performing minimization as the separate step

on the CPU-only.

The new problem have been arrisen when I add the barostat to my system on

the 6.3 step

# constant pressure

langevinPiston on

langevinPistonTarget 1.01325

langevinPistonPeriod 200.0

langevinPistonDecay 50.0

langevinPistonTemp $temp

from the beginning of this step the bi-layer have been increased in XY

plane rapidly and shrunk in the Z plane ( this simulation have been

performed with GPU). How this issue could be solved ?

2013/9/9 James Starlight <jmsstarlight_at_gmail.com>

*> I've just tried to make such minimization + equilibration in the different
*

*> steps
*

*> with that system
*

*> http://www.charmm-gui.org/?doc=input/membrane_only&time=1378378701
*

*>
*

*> but unfortunately after minimization my system have been crashed during
*

*> beginning of the production run (
*

*>
*

*> James
*

*>
*

*>
*

*> 2013/9/9 Cesar Millan <pachequin_at_gmail.com>
*

*>
*

*>> Hi,
*

*>>
*

*>> I really don't know, I just made that changes and it worked.
*

*>>
*

*>> Best regards.
*

*>>
*

*>> Cesar
*

*>>
*

*>>
*

*>> ############################
*

*>> César Millán Pacheco
*

*>> Facultad de Ciencias
*

*>> Universidad Autonoma del Estado de Morelos
*

*>> Tel: 777 3297020
*

*>> Fax: 777 3207040
*

*>> email: cmp_at_uaem.mx
*

*>> pachequin_at_gmail.com
*

*>>
*

*>>
*

*>>
*

*>> On Sun, Sep 8, 2013 at 11:52 PM, James Starlight <jmsstarlight_at_gmail.com>wrote:
*

*>>
*

*>>> Cesar, thank you for suggestion!
*

*>>>
*

*>>> Should I make any extra changes to the minim.inp file (made based on the
*

*>>> step6.1 template )?
*

*>>>
*

*>>> Is it possible to turned-off GPU-regime during some equilibration step ?
*

*>>> I'd like to check if the possible soursse of such errors in GPU.
*

*>>>
*

*>>> James
*

*>>>
*

*>>>
*

*>>> 2013/9/9 Cesar Millan <pachequin_at_gmail.com>
*

*>>>
*

*>>>> I dont turn off the gpu regime. I just create 3 new files using
*

*>>>> charmm-gui input files as templates. On step6.1.equ...inp, I separate it on
*

*>>>> two files step6.1.equilibration_min.inp and step6.1.equilibration_din.inp.
*

*>>>> After that on step6.1...min.inp i delete the "run ...." line and on
*

*>>>> step6.1...din.inp I delete those lines that implies a minimization process.
*

*>>>> You have to check that the names of step6.1....min.inp are the input names
*

*>>>> for step6.1....din.inp.
*

*>>>>
*

*>>>> Hope this helps.
*

*>>>>
*

*>>>> Cesar
*

*>>>>
*

*>>>>
*

*>>>>
*

*>>>> ############################
*

*>>>> César Millán Pacheco
*

*>>>> Facultad de Ciencias
*

*>>>> Universidad Autonoma del Estado de Morelos
*

*>>>> Tel: 777 3297020
*

*>>>> Fax: 777 3207040
*

*>>>> email: cmp_at_uaem.mx
*

*>>>> pachequin_at_gmail.com
*

*>>>>
*

*>>>>
*

*>>>>
*

*>>>> On Sun, Sep 8, 2013 at 12:04 PM, James Starlight <
*

*>>>> jmsstarlight_at_gmail.com> wrote:
*

*>>>>
*

*>>>>> Cesar,
*

*>>>>>
*

*>>>>> could you tell me how should I run my simulation in gpu turned off
*

*>>>>> regime ? I've not found this in man (
*

*>>>>>
*

*>>>>> James
*

*>>>>>
*

*>>>>>
*

*>>>>> 2013/9/8 Cesar Millan <pachequin_at_gmail.com>
*

*>>>>>
*

*>>>>>> Hi, I've done this kind of systems before on GPUs. You have to
*

*>>>>>> separate minimization and dynamics.
*

*>>>>>> Run the minimization process with the NAMD CPU version and the
*

*>>>>>> dynamics with the NAMD GPU version.
*

*>>>>>>
*

*>>>>>> best regards.
*

*>>>>>>
*

*>>>>>> Cesar
*

*>>>>>>
*

*>>>>>>
*

*>>>>>>
*

*>>>>>> ############################
*

*>>>>>> César Millán Pacheco
*

*>>>>>> Facultad de Ciencias
*

*>>>>>> Universidad Autonoma del Estado de Morelos
*

*>>>>>> Tel: 777 3297020
*

*>>>>>> Fax: 777 3207040
*

*>>>>>> email: cmp_at_uaem.mx
*

*>>>>>> pachequin_at_gmail.com
*

*>>>>>>
*

*>>>>>>
*

*>>>>>>
*

*>>>>>> On Sun, Sep 8, 2013 at 11:44 AM, James Starlight <
*

*>>>>>> jmsstarlight_at_gmail.com> wrote:
*

*>>>>>>
*

*>>>>>>> It seems that problem was not in cholesterol
*

*>>>>>>>
*

*>>>>>>> E.g I've tried to equilibration this simplest system
*

*>>>>>>>
*

*>>>>>>> http://www.charmm-gui.org/?doc=input/membrane_only&time=1378628752
*

*>>>>>>>
*

*>>>>>>> and after long minimization I've obtained error
*

*>>>>>>>
*

*>>>>>>> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 30000
*

*>>>>>>> WRITING COORDINATES TO DCD FILE AT STEP 30000
*

*>>>>>>> WRITING COORDINATES TO RESTART FILE AT STEP 30000
*

*>>>>>>> FINISHED WRITING RESTART COORDINATES
*

*>>>>>>> WRITING VELOCITIES TO RESTART FILE AT STEP 30000
*

*>>>>>>> FINISHED WRITING RESTART VELOCITIES
*

*>>>>>>> TCL: Setting parameter numsteps to 90000000
*

*>>>>>>>
*

*>>>>>>> TCL: Original numsteps 90000000 will be ignored.
*

*>>>>>>> TCL: Running for 25000 steps
*

*>>>>>>> REASSIGNING VELOCITIES AT STEP 30000 TO 310 KELVIN.
*

*>>>>>>> colvars: Writing the state file
*

*>>>>>>> "step6.1_equilibration.restart.colvars.state".
*

*>>>>>>> colvars: Synchronizing (emptying the buffer of) trajectory file
*

*>>>>>>> "step6.1_equilibration.colvars.traj".
*

*>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 14039!
*

*>>>>>>>
*

*>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 8959!
*

*>>>>>>>
*

*>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 66!
*

*>>>>>>>
*

*>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 15321!
*

*>>>>>>>
*

*>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 13670!
*

*>>>>>>>
*

*>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 9380!
*

*>>>>>>>
*

*>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 5019!
*

*>>>>>>>
*

*>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 11279!
*

*>>>>>>>
*

*>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 7260!
*

*>>>>>>>
*

*>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 18406!
*

*>>>>>>>
*

*>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>> ERROR: Exiting prematurely; see error messages above.
*

*>>>>>>> ====================================================
*

*>>>>>>>
*

*>>>>>>>
*

*>>>>>>> I'm not sure if it possible to run simulation purely with the CPU
*

*>>>>>>> (turned off GPU) on my machine
*

*>>>>>>> Typically I run simulation with GPU by means of
*

*>>>>>>> namd2 +idlepoll +p4 +devices 0 ./step6.2_equilibration.inp
*

*>>>>>>>
*

*>>>>>>> May be some extra parameters should be provided in the conf file
*

*>>>>>>> when I simulate with GPU? E.g I suppose that some addition should be added
*

*>>>>>>> to the PBC as well as PME options.
*

*>>>>>>>
*

*>>>>>>> James
*

*>>>>>>>
*

*>>>>>>>
*

*>>>>>>> 2013/9/8 Sunhwan Jo <sunhwan_at_uchicago.edu>
*

*>>>>>>>
*

*>>>>>>>> James,
*

*>>>>>>>>
*

*>>>>>>>> Can you try with CPU version of NAMD?
*

*>>>>>>>>
*

*>>>>>>>> Sunhwan
*

*>>>>>>>>
*

*>>>>>>>> Sent from my iPhone
*

*>>>>>>>>
*

*>>>>>>>> On Sep 8, 2013, at 12:04 AM, "James Starlight" <
*

*>>>>>>>> jmsstarlight_at_gmail.com> wrote:
*

*>>>>>>>>
*

*>>>>>>>> Emilia,
*

*>>>>>>>>
*

*>>>>>>>> I've already tried to increase minimization step number but result
*

*>>>>>>>> was the same.
*

*>>>>>>>>
*

*>>>>>>>> Briefly I've just tried to minimize my system (for example the
*

*>>>>>>>> system which I've shown or also I have the same system with reduced water
*

*>>>>>>>> layers) during equilibration step6.1 with namd 2.9(gpu-simulation regime).
*

*>>>>>>>> By the way what other options of the minimization can I change besides step
*

*>>>>>>>> number as well as integrator timestep (e.g can I vary gradient degree or
*

*>>>>>>>> minimization algorithm )?
*

*>>>>>>>>
*

*>>>>>>>> James
*

*>>>>>>>>
*

*>>>>>>>>
*

*>>>>>>>> 2013/9/7 Emilia Wu <emilia.l.wu_at_gmail.com>
*

*>>>>>>>>
*

*>>>>>>>>> You can minimize more steps before dynamics starts. The default
*

*>>>>>>>>> number in the input might be too small for your big system.
*

*>>>>>>>>>
*

*>>>>>>>>> Emilia
*

*>>>>>>>>>
*

*>>>>>>>>> On Sep 7, 2013, at 4:04 AM, James Starlight wrote:
*

*>>>>>>>>>
*

*>>>>>>>>> Emillia,
*

*>>>>>>>>>
*

*>>>>>>>>> I've tried to launch simulation from the files produced by
*

*>>>>>>>>> charm-gui but simulation have crashed on the beginning of the first
*

*>>>>>>>>> equilibration step after long minimization with the error
*

*>>>>>>>>>
*

*>>>>>>>>> TCL: Original numsteps 90000000 will be ignored.
*

*>>>>>>>>> TCL: Running for 25000 steps
*

*>>>>>>>>> REASSIGNING VELOCITIES AT STEP 0 TO 303.15 KELVIN.
*

*>>>>>>>>> Pe 2 has 36 local and 36 remote patches and 972 local and 972
*

*>>>>>>>>> remote computes.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4962!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 5678!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 2288!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 5370!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3089!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3759!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 20746!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 14993!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 2681!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4697!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1669!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1634!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4731!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 2191!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 6835!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 942!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 11615!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3217!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 7862!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1920!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 723!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1030!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 2733!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 262!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 336!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1259!
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1201!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3491!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 5287!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 145!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 6863!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 7462!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1811!
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 397!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 854!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1453!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1792!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 8914!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 10618!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3135!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 7368!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 13152!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 6171!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 8533!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 21871!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 9658!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1715!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 2824!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 12533!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 8990!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 751!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4164!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 6875!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 175!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1156!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 455!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 9569!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1535!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 435!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 7012!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 5552!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3525!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3266!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 256!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 6265!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 3155!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 2209!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 24!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4392!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4495!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 4751!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 552!
*

*>>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
*

*>>>>>>>>> ERROR: Exiting prematurely; see error messages above.
*

*>>>>>>>>>
*

*>>>>>>>>>
*

*>>>>>>>>> It looks like my system have not been equilibrated properly and I
*

*>>>>>>>>> have the same eror only in case of big systems. How I could fix it?
*

*>>>>>>>>>
*

*>>>>>>>>> James
*

*>>>>>>>>>
*

*>>>>>>>>>
*

*>>>>>>>>>
*

*>>>>>>>>> 2013/9/7 Sunhwan Jo <sunhwan_at_uchicago.edu>
*

*>>>>>>>>>
*

*>>>>>>>>>> James,
*

*>>>>>>>>>>
*

*>>>>>>>>>> My labmate has downloaded your files and ran step6.1 input
*

*>>>>>>>>>> using NAMD_2.9_Linux-x86_64-TCP/namd2. We didn't find any problems with the
*

*>>>>>>>>>> minimization and it was working well in our test.
*

*>>>>>>>>>>
*

*>>>>>>>>>> Sunhwan
*

*>>>>>>>>>>
*

*>>>>>>>>>> On Sep 6, 2013, at 11:24 AM, James Starlight <
*

*>>>>>>>>>> jmsstarlight_at_gmail.com> wrote:
*

*>>>>>>>>>>
*

*>>>>>>>>>> Dear all !
*

*>>>>>>>>>>
*

*>>>>>>>>>> Thanks for suggestions!
*

*>>>>>>>>>>
*

*>>>>>>>>>> I've mentioned in the adjacent topic the problem of minimization
*

*>>>>>>>>>> for the system consisted of many lipids + water (produced by charm_gui).
*

*>>>>>>>>>>
*

*>>>>>>>>>> Briefly when I try to minimize clashes in big systems ( many
*

*>>>>>>>>>> lipids + solvent) the minimization didt work ( its looks like all atoms
*

*>>>>>>>>>> were frozen during whole minimization trajectory so the clashes didnt
*

*>>>>>>>>>> resolved ).
*

*>>>>>>>>>>
*

*>>>>>>>>>> When I try to minimize the same system without water (only
*

*>>>>>>>>>> lipids)- there were no problem at all (the lipid tales constantly moves
*

*>>>>>>>>>> during minimization resolving clashes between them) .
*

*>>>>>>>>>>
*

*>>>>>>>>>> To fix this problem I've tried to add FIX ATOMS to all water
*

*>>>>>>>>>> according to tutorial but the problem have not been solved in case of big
*

*>>>>>>>>>> systems. How I should minimize it ?
*

*>>>>>>>>>>
*

*>>>>>>>>>>
*

*>>>>>>>>>> 2013/9/6 Sunhwan Jo <sunhwan_at_uchicago.edu>
*

*>>>>>>>>>>
*

*>>>>>>>>>>> James
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> CHARMM-GUI generates step_assembly.xplor.psf, which can be
*

*>>>>>>>>>>> used in NAMD. Perhaps this file is not displayed on webpage. You can
*

*>>>>>>>>>>> download every file generated by GUI by using "download .tgz" link on the
*

*>>>>>>>>>>> upper right corner of the webpage.
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> Sunhwan
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> Sent from my iPhone
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> On Sep 6, 2013, at 6:35 AM, "James Starlight" <
*

*>>>>>>>>>>> jmsstarlight_at_gmail.com> wrote:
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> Dear Namd Users!
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> I've already seen similar topic previously but didn't find any
*

*>>>>>>>>>>> possible solution.
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> How I could use charm gui outputs to generate namd psf file of
*

*>>>>>>>>>>> the generated membrane ? In my case charm gui generated 6 files
*

*>>>>>>>>>>>
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> http://www.charmm-gui.org/?doc=input/membrane_only&time=1378378701
*

*>>>>>>>>>>>
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> Equilibration Step1: step6.1_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.1_equilibration.inp> Equilibration
*

*>>>>>>>>>>> Step2: step6.2_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.2_equilibration.inp> Equilibration
*

*>>>>>>>>>>> Step3: step6.3_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.3_equilibration.inp> Equilibration
*

*>>>>>>>>>>> Step4: step6.4_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.4_equilibration.inp> Equilibration
*

*>>>>>>>>>>> Step5: step6.5_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.5_equilibration.inp> Equilibration
*

*>>>>>>>>>>> Step6: step6.6_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.6_equilibration.inp>
*

*>>>>>>>>>>> but how I can create psf from that data?
*

*>>>>>>>>>>>
*

*>>>>>>>>>>>
*

*>>>>>>>>>>> James
*

*>>>>>>>>>>>
*

*>>>>>>>>>>>
*

*>>>>>>>>>>
*

*>>>>>>>>>>
*

*>>>>>>>>>
*

*>>>>>>>>>
*

*>>>>>>>>
*

*>>>>>>>
*

*>>>>>>
*

*>>>>>
*

*>>>>
*

*>>>
*

*>>
*

*>
*

**Next message:**Aron Broom: "Re: NAMD CUDA performance"**Previous message:**Vlastimil ZĂma: "NAMD CUDA performance"**Maybe in reply to:**Sunhwan Jo: "Re: charm-gui membrane builder"**Next in thread:**James Starlight: "Re: charm-gui membrane builder"**Reply:**James Starlight: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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