[gmx-users] molecules blowing up

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Feb 20 09:33:08 CET 2006

Hi Yegor,

To start with, please refrain from sending mails to persons in stead of to
the mailing list, in particular when the person is also on the mailing list
(now I got this message twice!). On the mailing list there is a higher
probability of getting a sensible answer, since there are more people
reading that than there are reading my mailbox (I hope).

It is not enough to only define a bond. where two atoms are bonded in a
larger construct, there are also angles, dihedrals and possibly improper
dihedrals. Furthermore, the atoms on either side of the bond should not
'see' each other in any other way than through the bonded terms. They have
to be excluded. It can be that your sulfur atom has a non-bonded interaction
with a nearby atom, which it shouldn't have, giving rise to a large force.

Best regards,


On 2/19/06, X.Periole <X.Periole at rug.nl> wrote:
> On Sun, 19 Feb 2006 09:22:41 -0800 (PST)
>   Yegor Isakov <gromacs_problems at yahoo.com> wrote:
> > I appreciate if  anybody could answer my question?
> > ,
> >       My molecules continue blowing out. I have got a
> >peptide where a  carbonyl group is connected to cysteine
> >through S atom (-S-CO-). I inserted my topology (the
> >whole set including peptide.top, peptide.gro, and
> >posre.itp ) into gmxdemo script (water) and run it the
> >same way as the demo cpeptide. My molecule blows out at
> >the third step of the run.  In the program output I have
> >got a message that the force is concentrated on the S
> >atom.
> >        I have got another molecule where carbonyl group
> >was attached to protein through NH group (-NH-CO-). This
> >bond is stable enough and the molecule runs fine up to
> >3000 steps.
> > Thus, I concluded that the problem is that (-S-CO-)
> >bond. Actually I did not find  this bond in the libraries
> >and I introduced it myself into my topology by just
> >adding the the physical length of the bond. I believe
> >that's not enough.
> >      My question is: what I need to do to introduce into
> >my MD model a new bond that was not previously described
> >in those libraries? The manual does not cover this topic
> >explicitly.
> >
> it is called distance restraints, 4.2.14 in manual gmx3.2.
> XAvier
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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