**From:** Sunhwan Jo (*sunhwan_at_uchicago.edu*)

**Date:** Wed Sep 11 2013 - 17:41:02 CDT

**Next message:**Rehan Zafar: "Patching protein with phosphoserine, phosphothreonine and phosphotyrosine patches"**Previous message:**James Starlight: "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"**Reply:**James Starlight: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

James,

I do not encounter problems equilibrating bilayer in general. You should be careful when very high concentration of cholesterol or highly irregular shape of protein is used, because lipid tails could penetrate the protein surface or cholesterol ring system.

If you read your input, step6.1 and step6.2 perform NVT simulation, and step6.3 and later perform NPT simulations. Thus, your simulation system can expand during step6.3. So, no wonder you could workaround this problem by using "useConstantArea" option.

To me, the only remaining question would be whether the expansion is expected or not. I realized you are referring to a new system below. I have downloaded your system and it seems the system is not properly neutralized and have total charge of -160e. I never have run a system that is not properly neutralized, so I'm not sure if the problem you having is the consequence of that or not.

Is there any reason you have decided not to include ions? Perhaps NAMD can takes care of non-neutral simulation system, but those charges (-80e in each leaflet) repel each other and make your system to expand rapidly.

Best,

Sunhwan

On Sep 11, 2013, at 3:15 PM, James Starlight <jmsstarlight_at_gmail.com<mailto:jmsstarlight_at_gmail.com>> wrote:

Sunhwan,

have you any problems with my bilayer during equilibration? Briefly using charm-gui input files on the 6.3 stage my bilayer rapidly expanded in the X plane and shrunk in the Z plane and during 6/4 stage the simulation have been crushed with PBC dimensions error.

This particularly have been fixed by inclusion in the conf file useConstantArea option

instead of useConstantRatio. All those simulations have been performed with latest NAMD on CUDA.

James

2013/9/11 Sunhwan Jo <sunhwan_at_uchicago.edu<mailto:sunhwan_at_uchicago.edu>>

James,

I'm the main authors of CHARMM-GUI membrane builder and our NAMD input files has been throughly tested for NAMD 2.8 and above. One of my colleague even tested with your simulation system using NAMD 2.9 (CPU), so I'm not certain why you having such problem. Let me know if there is anything that we can do to help.

Thanks,

Sunhwan

On Sep 11, 2013, at 12:20 PM, James Starlight <jmsstarlight_at_gmail.com<mailto:jmsstarlight_at_gmail.com>> wrote:

My problem have been solved via adding below term to the conf file

useConstantArea yes ;

instead of

useConstantRatio yes ; # which was presented on the default charm-gui conf file.

I'm not sure if this is possible to make such changes to the NON equilibrated bilayers but this prevent crash with PBC error

also could my problem be solved providing softer coupling to the pressure bath increasing below two params ?

langevinPistonPeriod 200.0

langevinPistonDecay 50.0

Finally does anybody knows some pre-equlibrated bilayers with suitable namd inputs ?

James

2013/9/10 James Starlight <jmsstarlight_at_gmail.com<mailto:jmsstarlight_at_gmail.com>>

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<mailto: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<mailto: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<mailto:cmp_at_uaem.mx>

pachequin_at_gmail.com<mailto:pachequin_at_gmail.com>

On Sun, Sep 8, 2013 at 11:52 PM, James Starlight <jmsstarlight_at_gmail.com<mailto: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<mailto: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<mailto:cmp_at_uaem.mx>

pachequin_at_gmail.com<mailto:pachequin_at_gmail.com>

On Sun, Sep 8, 2013 at 12:04 PM, James Starlight <jmsstarlight_at_gmail.com<mailto: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<mailto: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<mailto:cmp_at_uaem.mx>

pachequin_at_gmail.com<mailto:pachequin_at_gmail.com>

On Sun, Sep 8, 2013 at 11:44 AM, James Starlight <jmsstarlight_at_gmail.com<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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:**Rehan Zafar: "Patching protein with phosphoserine, phosphothreonine and phosphotyrosine patches"**Previous message:**James Starlight: "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"**Reply:**James Starlight: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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