[gmx-users] A question about pressure coupling and random seed generator in microsecond long simulations

[anu chandra]

Dear Gromcas users,

I have been following the Gromcas tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/08_MD.html
) for setting up and running MD simulations of membrane proteins. I am
aiming for a microsecond long simulation. In this regard, I have few
queries about some of the parameters in mdp file used for production run in
membrane protein tutorial.

1. Is it required to use NPT (pressure coupling) rather than NVT for the
production run if the system is already extensively equilbrated in NPT
ensemble before taking to the production stage?

2. The literature suggests to set the random seed generator 'on' for a
better sampling during simulation. I have noticed that the 'gen_vel = no'
in the mdp file used for production run in the tutorial. I just wonder,
will it be safe to set the 'gen_vel=yes' during the production run using
Gromcas.


Many thanks in advance

Anu