[gmx-users] ngmx: Segmentation fault
spoel at xray.bmc.uu.se
Fri Aug 29 18:46:01 CEST 2003
On Fri, 2003-08-29 at 18:17, Albert Sun wrote:
> Hi, David,
> Do you know what is the reason that atoms explod?
> Is it because that I did not include bond force and constraints or
> other wrong parameters?
Anything, charged atoms with no van der waals or something like that.
Something in your topology. If you give all atoms zero charge and a
reasonable vanderwaals params it will work fine.
> David <spoel at xray.bmc.uu.se> wrote:
> On Thu, 2003-08-28 at 23:07, Albert Sun wrote:
> > Dear David van der Spoel,
> > I am testing a simple case, and prepared top and gro
> files as
> > attached, when I ran EM.mdp and 9atom.mdp, and see
> ngmx, it has the
> > error: segmentation fault.
> > (em.mdp file is attached in another email)
> > Could you help me to have a look?
> I see a system of 9 atoms in a plane which explodes
> after roughly 100 fs
> (I decreased nstxout to 5 to see it).
> If you do not see that, then I suggest you try to run
> it on a Linux or
> Unix box first. By the way, ngmx won't work on a DOS
> Groeten, David.
> Dr. David van der Spoel, Dept. of Cell and Molecular
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org
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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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