**From:** Grace Brannigan (*gracebrannigan_at_gmail.com*)

**Date:** Sun Sep 08 2013 - 01:02:31 CDT

**Next message:**Hailey Bureau: "explicit NVT simulation"**Previous message:**Cesar Millan: "Re: charm-gui membrane builder"**In reply to:**James Starlight: "Re: charm-gui membrane builder"**Next in thread:**James Starlight: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi James,

CHARMM-GUI membrane builder can sometimes place acyl chains through rings

contained in aromatic residues, cholesterol, etc. Have you checked for

this, if you have cholesterol in your system? It is a possible source of

RATTLE errors.

cheers,

Grace

On Sun, Sep 8, 2013 at 12:56 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:**Hailey Bureau: "explicit NVT simulation"**Previous message:**Cesar Millan: "Re: charm-gui membrane builder"**In reply to:**James Starlight: "Re: charm-gui membrane builder"**Next in thread:**James Starlight: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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