[gmx-users] unstable system
Shima Arasteh
shima_arasteh2001 at yahoo.com
Fri Apr 19 19:18:51 CEST 2013
Lets check the minim.mdp settings:
( ff applied is charmm36)
define = -DPOSRES
integrator = steep
emtol = 100.0
emstep = 0.01
nsteps = 50000
nstlist = 1
ns_type = grid
rlist = 1.2
rlistlong = 1.4
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2
vdwtype = switch
rvdw_switch = 1.0
pbc = xyz
I would be grateful for your suggestions.
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 8:42 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:55 AM, Shima Arasteh wrote:
> 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.
>
>
It's a waste of time to delve into hypotheticals. Please try the advice you've
been given and report back if needed. Crashes like you are seeing are almost
invariably due to poor starting configuration. Thorough EM solves that problem.
If, for some reason, that doesn't work, we will continue to diagnose.
-Justin
>
> 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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