[gmx-users] unstable system
shima_arasteh2001 at yahoo.com
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?
----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, April 19, 2013 7:58 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:26 AM, Shima Arasteh wrote:
> 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.
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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