[gmx-users] how to increase the number of

[Mark Abraham]

Afonso Duarte wrote:
> Dear All,
>  
> I am using GROMACS 3.3.1 and i setup a simulation to run in 2 nodes of a 
> workstation. It is running OK however now i have two extra nodes 
> available to use in the same box and i would like to speed up the sim by 
> using them.
>  
> Is there any way to increase the number of nodes under use ?
>  
> I tried tpbconv to extend the sim and increase the np vaue but it did 
> not worked.

The other way to do a restart is to get your original .mdp file (check 
the values of gen_seed and unconstrained_start are appropriate), and 
your current .trr, .edr and any appropriate .gro (it's just used for 
atom names) and feed them to grompp with whatever -n flag you want to 
use. I expect this will not be reproducible with a tpbconv restart 
(particularly with PME) but you'll still be sampling the same ensemble 
within the error of the MD approximation.

Mark