[gmx-users] Position Restrain md

[Jamie Seyed]

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??
(2) In this case how program recognize which one should restrain and which
one not, because it included all??
(3) This step is required for every system or only proteins??
(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??
(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
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