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

**Date:** Sun Sep 08 2013 - 23:52:00 CDT

**Next message:**Kenno Vanommeslaeghe: "Re: explicit NVT simulation"**Previous message:**Bennion, Brian: "RE: VDW energy is negative but total energy is positive"**Maybe in reply to:**Sunhwan Jo: "Re: charm-gui membrane builder"**Next in thread:**James Starlight: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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:**Kenno Vanommeslaeghe: "Re: explicit NVT simulation"**Previous message:**Bennion, Brian: "RE: VDW energy is negative but total energy is positive"**Maybe in reply to:**Sunhwan Jo: "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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