[gmx-users] Extending simulation with -pd

Peter C. Lai pcl at uab.edu
Fri Mar 2 18:28:26 CET 2012

On 2012-03-02 05:25:01PM +0000, Steven Neumann wrote:
> Dear Gmx Users,
> I run nvt simulation with small timestep with implicit solvent for 500 ps.
> I used particle decomposition for this run (-pd). No I want to extend my
> simulation with different mdp file from the previous nvt using:
> grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt
> mdrun -s new.tpr (-pd?)
> This is my question - shall use -pd option again or will it be considered
> automatically?

The manual entry for mdrun tells you what commandline switches are
considered enabled by default. I don't think -pd is one of them so you 
will have to specify it every time (it's safer to specify it anyway).

Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
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