[gmx-users] unstable system
shima_arasteh2001 at yahoo.com
Sun Apr 7 19:58:09 CEST 2013
Yes, some letters were transferred by mistakes to email.
Yes, I am using charmm36. Also the rvdw_switch was correct the same as you wrote 1.0 in last email.
Now, I am wondering what the solution is in such cases of facing such an error? Would you please let me know your suggestions?
Many thanks for your replies.
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:
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ========================================
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