[gmx-users] MD after equilibration phase

Peter C. Lai pcl at uab.edu
Fri Apr 6 09:12:58 CEST 2012

On 2012-04-06 11:05:51AM +0400, James Starlight wrote:
> Dear Gromacs users!
> I have small question about order of the runs and input data.
> Ussually I do 2 equilibration phases and subsequent productive phase in the
> conditions wich are equal to the last equilibration phase ( e.g often this
> is npt ).
> In the second equil.mdp and md.mdp there is option
> continuation             = yes
> which means that there have been previous phases of the simulation from
> wich  coordinates and velocities should be taken.
> As I understood the coordinates is taken from .gro file but from what file
> the velocities must be providen ? Does it .cpt checkpoint file from
> previous run? In some cases I've forgotten to define -t npt.cpt for my MD
> run providing only coordinates in GRO file, topology and md.mdp but I have
> not seen any errors in such simulation due to absence of that .cpt and
> GROMPP never remind me of the absense of this file. What exactly is in that
> .cpt file and from wich source the velocities from equilibration phase are
> taken ?

continuation = yes is telling LINCS that it is a continuation and
it should not attempt to refit the constrained bonds on the first pass.

The coords, velocities, state, and box information are taken either from the 
cpt file or you can specify the previous .trr and it will take the last frame
from that and use it. If you used the output gro file without -t, then
it will take coordinates and velocities from the .gro but the problem there
is the limited precision (3 decimal points for each).

Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
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