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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