[gmx-users] unstable system
jalemkul at vt.edu
Sun Apr 7 20:23:13 CEST 2013
On Sun, Apr 7, 2013 at 1:58 PM, Shima Arasteh
<shima_arasteh2001 at yahoo.com>wrote:
> 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.
I would suggest you take great care to provide accurate information,
especially when it is requested of you. I thought I had identified a
mistake that would have lead to instability. It turns out that you posted
something fictitious and it feels a bit like I wasted my time. If you want
free help, make it easy for those who want to help you to do so.
> Now, I am wondering what the solution is in such cases of facing such an
> error? Would you please let me know your suggestions?
I see no reason why a system that was previously stable for 10 ns to
suddenly become unstable. Monitor energy terms very closely, and try
reducing the time step to 1 fs for a period of time.
> 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>
> 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
> ; 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
> >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.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540)
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