Thank you very much for your clear reply.
Best regards,
Julian Garrec
Le 25/05/12 17:17, Mark Abraham a écrit :
On 25/05/2012 7:44 PM, Julian Mondon-Garrec wrote:
Hi all,
I am trying to get the electrostatic forces acting on each atom as a
function of time. I have checked the list and all the suggestions are
based on rerunning the simulation. Is there not an easy way to print
these forces on the fly ?
You can print the whole force "on the fly" with nstfout, but you
cannot decompose it.
If not, what is the cleanest way to remove bonded and vdw components
from the forces ? One option could be to set all the unwanted
interaction to zero in the topology file but I am wondering if there
is a safer alternative.
The code permits such a "safe" alternative, by not setting
GMX_FORCE_BONDED, but there is no way to access that setting from the
command line. The best you can easily do is mdrun -rerun with
parameters zeroed.
Mark
--
Julian Garrec, post-doc
Tel: ++41 (0)21 69 303 27
Web: https://sites.google.com/site/juliangarrec/
Laboratory of Computational Chemistry and Biochemistry
BCH 4201 Ecole Polytechnique Fédérale de Lausanne
CH-1015 Lausanne
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