[gmx-users] Re:Question regarding Gromacs

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Sep 29 09:50:34 CEST 2008


> Thanks for the reply, what may be the reason GROMACS became great?

Check the JCC 2005 paper: http://www.ncbi.nlm.nih.gov/pubmed/16211538

>   sometimes though system explodes it will generate energy minimisation
> output.gro file we cant use this file for further run?

Need more information..., what did you try to do? Did you do EM? Check
for overlaps, go through your system carefully, don't stick your head
in the sand and continue the simulation. Mind you that MD programs
adhere to the Rubbish-in Rubbish-out protocol (RRP :p).



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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