[gmx-users] Position Restrain md

[Mark Abraham]

Jamie Seyed wrote:
> Dear all,
> I have questions regarding the position restrain md. I tried to find the
> answer of my questions from the mailing list, but it is not clear yet.
> In the fws tutorial when it says (in the pr.mdp)
> tc_grps=Protein   non-protein
> (1) Doesn't that mean everything in the system? I think for this case we can
> simply write "system" because system is made by protein and non-protein??

It includes the whole system, but it is often a good idea not to couple 
groups of heterogeneous heat capacity to the same thermostat. That said, 
if the groups are too small, you get other problems. See also 
http://oldwiki.gromacs.org/index.php/temperature_coupling

> (2) In this case how program recognize which one should restrain and which
> one not, because it included all??

Temperature coupling has no linkage with position restraints. You 
defined the latter in your .top file.

> (3) This step is required for every system or only proteins??

It may or may not be useful in achieving stable equilibration for any 
system. See 
http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation

> (4) If I want to make an index file and I specify a group that need to be
> constrained, in the generated index file I will get system and all its parts
> and an extra part for my specific part that need to be constrain...Is that
> ok??

"constraints" are different from "restraints" in GROMACS usage. make_ndx 
does allow you to generate new index groups, but you will need to 
(re-)read the relevant manual sections to understand that neither of 
these algorithms uses index groups. (Or to prove my memory wrong!)

> (5) In my case I have a molecule (MOL) and water (SOL), for position
> restrain md should I use "tc_grps=MOL   SOL" (according to fws tutorial) or
> I need only write "tc_grps=MOL"??  Many Thanks in Advance/Jamie

The latter won't work, for all atoms must be members of a 
temperature-coupling group if any are.

What you actually need is a clear understanding of your strategic 
objective. Hopefully some of the links will move you towards that.

Mark