[gmx-users] distance restraints in Gromacs 4.0.4
igladich at purdue.edu
Wed Apr 8 02:52:50 CEST 2009
I have found a problem for the distance constraint in the version
4.0.4 of gromacs.
I am trying to simulate a water droplet around an ion. To do that I use
a distance restraint armonic potential (pag.66, manual version 4).
During my simulation the shape of my sphere fluctuating too much and
many molecules leave the sphere even if the restoring force is big (I
use for restraint armonic potential a constant k=1e4 KJ mol^-1 nm^-2 ).
The problem disappear if I run the exactly same simulation with gromacs
3.3.3.:the spherical shape is always conserve and no molecules leave the
Furthermore, if I am trying to run droplet larger than 1.0 nm radius
(e.g. 1.6 nm). These simulation at a certain point stop, giving me the
** glibc detected *** Dmdrun: munmap_chunk(): invalid pointer:
The same simulation in the version 3.3.3 runs without any problem.
Do you know what kind of problem could be?
Has the version 4.0.4 some problems with distance restrains?
Thank you in advance for any help or suggestion
Dreyfus Postdoctoral Fellow
Department of Chemistry
560 Oval Drive, box 140
IN 47906 USA
e-mail: igladich at purdue.edu
web page: http://web.ics.purdue.edu/~igladich/
More information about the gromacs.org_gmx-users