[gmx-users] large VCM(group rest)
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 2 14:19:45 CEST 2009
So if the system is exploding during energy minimization, then there is severe
atomic overlap somewhere in the system, as pointed out earlier. Have you
watched the trajectory? You have "nstxout = 1" so you might have a few usable
frames to watch and see where things are going wrong.
Another possibility - turn of position restraints. They could be restraining
some geometrically unstable configuration.
-Justin
Carla Jamous wrote:
> This is the mdp file i use for my energy minimization
>
> Thanks
> Carla
> ;
> ; 1W5B all-atom
> ; Input file
> ;
> cpp = /usr/bin/cpp
> define = -DPOSRES
> constraints = none
> integrator = steep
> nsteps = 500
> ;
> ; Energy minimizing stuff
> ;
> emtol = 1000.0
> emstep = 0.01
>
> nstcomm = 1
> ns_type = grid
> nstlist = 10
> nstxout = 1
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> vdwtype = cut-off
> rvdw = 1.4
> fourierspacing = 0.12
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
> On Fri, Oct 2, 2009 at 12:46 PM, Jochen Hub <jochen at xray.bmc.uu.se
> <mailto:jochen at xray.bmc.uu.se>> wrote:
>
> Carla Jamous wrote:
>
> Hi,
> when I get the error message: "water molecule cannot be
> settled",does it have to do with the SETTLE parameter in gromacs?
> If yes, does anyone know how to fix this?
>
> No, that probably means that you have clashes (atomic overlaps) in
> your system which cause huge forces. Track down which atoms cause
> the error message and remove the clashes.
>
> If that error message appeares during energy minimization, using
> flexible water may help. Define -DFLEXIBLE in the mdp file, and
> check in the spc/itp4p/tip3p.itp file if flexible water molecules
> are actually defined.
>
> Good luck,
> Jochen
>
>
>
>
> Carla
>
>
> On Thu, Oct 1, 2009 at 4:46 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Carla Jamous wrote:
>
> Hi,
> I have a problem, I'm running EM, it works but when it comes
> to doing position-restrained MD, it gives me this error
> message:
>
> Segmentation fault
> Large VCM(group System): -1293135642624.00000,
> 358859374592.00000, -846768177152.00000, T-cm: 6.13428e+26
>
> I searched the archives, it says to check-out:
> oldwiki.gromacs.org <http://oldwiki.gromacs.org>
> <http://oldwiki.gromacs.org>
> <http://oldwiki.gromacs.org>
>
> but this site doesn't exist anymore.
>
>
> All of the content has been moved to the new site, albeit a very
> different organization system. You should still be able to find
> it with a bit of digging.
>
>
> So please can anyone give me the answer to this problem?
>
>
> The problem is that your system is suddenly moving very fast,
> probably blowing up. Without a further description of the system
> and seeing your .mdp file, it's hard to say what the root
> problem is.
>
> -Justin
>
>
> Cheers,
> Carla
>
>
>
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> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> ---------------------------------------------------
> Dr. Jochen Hub
> Molecular Biophysics group
> Dept. of Cell & Molecular Biology
> Uppsala University. Box 596, 75124 Uppsala, Sweden.
> Phone: +46-18-4714451 Fax: +46-18-511755
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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