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

**Date:** Sat Sep 07 2013 - 04:04:10 CDT

**Next message:**Emilia Wu: "Re: charm-gui membrane builder"**Previous message:**dayanidhi mohanta: "VDW energy is negative but total energy is positive"**In reply to:**Sunhwan Jo: "Re: charm-gui membrane builder"**Next in thread:**Emilia Wu: "Re: charm-gui membrane builder"**Reply:**Emilia Wu: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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:**Emilia Wu: "Re: charm-gui membrane builder"**Previous message:**dayanidhi mohanta: "VDW energy is negative but total energy is positive"**In reply to:**Sunhwan Jo: "Re: charm-gui membrane builder"**Next in thread:**Emilia Wu: "Re: charm-gui membrane builder"**Reply:**Emilia Wu: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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