[gmx-users] unstable system

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Apr 19 17:55:09 CEST 2013 

All right.
And if minimization doesnt fix such a problem, what would be the solution?
However I have not tried it on my own system yet.


 
Sincerely,
Shima


----- Original Message -----
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>
Cc: 
Sent: Friday, April 19, 2013 8:22 PM
Subject: Re: [gmx-users] unstable system



On 4/19/13 11:43 AM, Shima Arasteh wrote:
> 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?
>

Whatever makes sense for your system.  There is no universal answer to how 
equilibration should be done.  If your simulation is crashing at step zero, I 
doubt that removing restraints will help in any way.

-Justin

>
>
> 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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