[gmx-users] large VCM(group rest)

[Carla Jamous]

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> 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>> 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>
>>
>>        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> | (540) 231-9080
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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>>
>> ------------------------------------------------------------------------
>>
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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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