[gmx-users] no pr.gro file for energy minimization
Peter C. Lai
pcl at uab.edu
Mon May 28 17:36:49 CEST 2012
A question: why do you not have a pr.gro? It should been output by the
mdrun of pr.tpr?
Anyway, yes you should be able to use -c pr.tpr. However you need to make
sure to use -t pr.trr or -t pr.cpt to ensure it uses the coordinates and
velocities from the end of the equilibration run. Even if you use -c pr.gro,
it is a good idea to use -t to ensure that it uses the full-precision
coordinates and velocities from the previous run.
The -c .gro/.tpr are at a minimum necessary for grompp to put atom names
into the new .tpr file that it generates.
On 2012-05-28 04:21:35PM +0100, Lara Bunte wrote:
> After equilibrating the water around my molecule I want to run the MD simulation. In my tutorial this is primed with:
> grompp -f run.mdp -p topol.top -c pr.gro -o run.tpr
> I don't have this pr.gro file but I have a pr.tpr file. Could I use this one? It seems GROMACS accepts this but I don't know whether this is good.
> I have this pr.tpr file because I used in the equilibrating the water procedure the command
> grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr
> Thanks for help
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Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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