[gmx-users] unstable system

[Justin Lemkul]

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     = 0.1
>

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

-- 

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

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