[gmx-users] define statement in mdp file

[Mark Abraham]

On Sat, Mar 23, 2013 at 7:25 PM, Shima Arasteh
<shima_arasteh2001 at yahoo.com>wrote:

> That's right.
> But I' d like to be sure about this fact that both restraints are applied.
> I see just 1 position restraints energy term in log file. Is just
> visualizing the trr file the only way of becoming sure that the headgroups
> and protein are restrained?
>

You can use the -pp flag with grompp to get a post-processed stand-alone
.mdp file that might illustrate what you wish to confirm. Otherwise,
gmxdump -s your.tpr will definitely have the information (but piecing
together the indexing to show which atoms have position restraints can be
painful).

And one more question is that, to eliminating the position restraints in
> MDRUN, is it supposed to reduce the force on atoms before mdrun gradually?
> Or it is ok to reduce it in MD step?
>

You can do whatever you like by varying the force constant between runs,
but an individual run will be on or off.

Mark