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

**Date:** Sat Sep 07 2013 - 23:56:42 CDT

**Next message:**Sunhwan Jo: "Re: charm-gui membrane builder"**Previous message:**Francesco Pietra: "About a REMD tutorial"**In reply to:**Emilia Wu: "Re: charm-gui membrane builder"**Next in thread:**Sunhwan Jo: "Re: charm-gui membrane builder"**Reply:**Sunhwan Jo: "Re: charm-gui membrane builder"**Reply:**Grace Brannigan: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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:**Sunhwan Jo: "Re: charm-gui membrane builder"**Previous message:**Francesco Pietra: "About a REMD tutorial"**In reply to:**Emilia Wu: "Re: charm-gui membrane builder"**Next in thread:**Sunhwan Jo: "Re: charm-gui membrane builder"**Reply:**Sunhwan Jo: "Re: charm-gui membrane builder"**Reply:**Grace Brannigan: "Re: charm-gui membrane builder"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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