[gmx-users] problem regarding total time elapsed

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jul 26 04:22:55 CEST 2007

gurpreet singh wrote:
> Hello users
> I am using gromacs 3.3 with 43a1 force field.
> My question is that if i run a simulation say for 50ns , Then if i 
> carried out another md after this one than its time should start from 
> ahead of 50  and not again from the beginning. but  in my case everytime 
> the time starts from the beginning.

It's doing this because you're telling it to do this. :-)

> I know its a very basic question which i should not ask from the 
> intelligentsia but this is irritating me from quiet a long time.
> so please tell me if this is a usual behaviour or some mistake is there 
> in the input file

You're using grompp for restarts, which is fine, but you need to be 
aware that there are heaps of input file options, some of which have 
default values. See section 7.3.3 of the manual. Easier than reworking 
your .mdp file all the time is to use tpbconv for restarts, as Alan 
suggested. See man tpbconv.

> After every run i am using the output gro file as an input for the next run

Hopefully it's not the only input! You only need a structure file for 
the atom names (or so)... everything else comes from trajectory and 
energy files.


More information about the gromacs.org_gmx-users mailing list