Re: [gmx-users] large VCM(group rest)

[Justin A. Lemkul]

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 <joc...@xray.bmc.uu.se 
<mailto:joc...@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
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@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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