[gmx-users] unstable system

Fri Apr 19 17:43:41 CEST 2013

Thanks for your reply.

I' d like to know if I need to remove all position restraints before MDRUN?means that the last step of npt should be done without position restraints?

Sincerely,
Shima

----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Friday, April 19, 2013 7:58 PM
Subject: Re: [gmx-users] unstable system

On 4/19/13 11:26 AM, Shima Arasteh wrote:
> Hi,
>
> I tried to equilibrate my system by setting timestep=1 fts and decreasing the position restraints step by step.
>
> But when I go to MDRUN step, it doesnt work and some pdb files are printed.
>
> what is printed in my log file is as follow:
>
>             Step           Time         Lambda
>                0        0.00000        0.00000
>
>     Energies (kJ/mol)
>              U-B    Proper Dih.  Improper Dih.      CMAP Dih.          LJ-14
>      8.34161e+04    5.57602e+04    7.65365e+02   -1.97155e+02    8.52248e+03
>       Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     -1.06644e+05    8.46716e+04   -5.77343e+03   -1.11612e+06   -2.67240e+05
>        Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
>     -1.26284e+06    6.13687e+05   -6.49154e+05    8.17667e+02   -1.08370e+02
>   Pressure (bar)   Constr. rmsd
>     -8.62031e+04    5.99322e-04
>
>
>
> Would you please give me any suggestions? Does my system need more equilibration yet? longer equilibration time?
> Whats the problem? My settings as sent you earlier seem fine, so whats the solution?
>
> Thanks for your suggestions. They would be appreciated.
>

The temperature is 817 K, indicating something is moving with a ridiculously 
high velocity that has been imparted by strong forces.  You have atoms 
overlapping somewhere.  Try more thorough energy minimization.

-Justin

>
>
> Sincerely,
> Shima
>
>
> ________________________________
>   From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Sunday, April 7, 2013 4:46 PM
> Subject: Re: [gmx-users] unstable system
>
>
>
>
>
>
>
>
> On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:
>
> Hi all,
>>
>>   I have a system of peptide/POPC/water/ions. The energy minimization and NVT steps has passed successfully. I ran NPT step for around 10 ns with restraints of protein and P atoms at first nano seconds and then removing them gradually.
>> I tried to go on MDRUN. I did not remove restraint of protein atoms completely and they are still restrained. When I run the mdrun command, I get error of "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" .
>> I know this error means an unstable system. When I visualized the written pdb files, I see some popc hydrogen atoms are broken and located between two leaflets which are separated by a gap. The protein seems ok, however I  don't get many pdb files to see.
>>
>>
>> As what I see in Diagnosing unstable system web page,
>> 1. it would be beneficial if one see what part of the system is unstable in first steps. As I saw, the unstable "POPC hydrogen atoms" are not fine.
>> 2. The single molecules are supposed to examine in water or vacuum too. I have passed this step successfully.
>> 3. I have not ignored any warning during the last steps.
>> 4. And my mdp files to run md is as follow:
>>
>> integrator    = md
>> dt        = 0.002
>> nsteps        = 5000000
>>
>>
>> ns_type        = grid
>> nstlist        = 5
>> rlist        = 1.2
>> rlistlong       = 1.4
>> rcoulomb    = 1.2
>> rvdw        = 1.2
>> pbc        = xyz
>> vdwtype         = switch
>> rvdw_switch     = 1.0
>>
>
> What force field are you using? CHARMM? In any case, the value of rvdw_switch does not make any sense. If you're using CHARMM, it should be 1.0.
>
> ; Parameters for treating bonded interactions
>> continuation    = yes
>> constraint_algorithm = LINCS    NCS / SHAKE)
>> constraints    = all-bonds    )
>> lincs_iter    = 1
>> lincs_order    = 4
>>
>> ; Parameters for treating electrostatic interactions
>> coulombtype    = PME        ; Long range electrostatic interactions treatment (cut-off, Ewald, PME)
>> pme_order    = 4        ; Interpolation order for PME (cubic interpolation is represented by 4)
>> fourierspacing    = 0.16        ; Maximum grid spacing for FFT grid using PME (nm)
>>
>> ; Temperature coupling parameters
>> tcoupl        = Nose-Hoover
>> tc-grps        = Protein_POPC Water_and_ions        ; Define groups to be coupled separately to temperature bath
>> tau_t        = 0.5    0.5             ; Group-wise coupling time constant (ps)
>> ref_t        = 310     310        ; Group-wise reference temperature (K)
>>
>> ; Pressure coupling parameters
>> pcoupl        = Parrinello-Rahman
>> pcoupltype    = semiisotropic
>> tau_p        = 2.0
>> ref_p        = 1.01325 1.01325
>> compressibility = 4.5e-5    4.5e-5
>>
>> ; Miscellaneous control parameters
>> ; Dispersion correction
>> DispCorr    = EnerPres
>> ; Initial Velocity Generation
>> gen_vel        = no
>> ; Centre of mass (COM) motion removal relative to the specified groups
>> nstcomm        = 1           y (steps)
>> comm_mode    = Linear
>> comm_grps    =Protein_POPC Water_and_ions    ; COM removal relative to the specified groups
>>
>>   Would you please let me know if these happen due to an improper equilibration? Do I need to extend the NPT step? Would that fix it?
>>
>>
>
> Aside from the above comment, there is nothing particularly wrong about the .mdp file aside from some odd characters here and there, which I will assume are nothing more than quirks of transferring to an email, as they otherwise would have triggered fatal errors in grompp.
>
> -Justin
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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