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

**Date:** Sun Sep 08 2013 - 11:44:04 CDT

**Next message:**Cesar Millan: "Re: charm-gui membrane builder"**Previous message:**Sunhwan Jo: "Re: charm-gui membrane builder"**In reply to:**Sunhwan Jo: "Re: charm-gui membrane builder"**Next in thread:**Cesar Millan: "Re: charm-gui membrane builder"**Reply:**Cesar Millan: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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:**Cesar Millan: "Re: charm-gui membrane builder"**Previous message:**Sunhwan Jo: "Re: charm-gui membrane builder"**In reply to:**Sunhwan Jo: "Re: charm-gui membrane builder"**Next in thread:**Cesar Millan: "Re: charm-gui membrane builder"**Reply:**Cesar Millan: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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