Thanks Peter for your reply actually, I did not think about that possibility because in the most windows, I have this small highly charged peptide out of the membrane. Moreover, in the last US windows, the peptide creates a defect and there are several water molecules inside the membrane. So, if I think about this fact, I associate the peptide with the SOL molecules, because of it charged nature... some questions come to my mind:
If I'll have a simple charged aminoacid or a bigger charged peptide, the definition for the tc_groups that you proposed me, would be the same (i.e. peptide_membrane)? I think that it could be a little tricky to see. I should be worried about the high temperature fluctuations if I choose the peptide as an individual tc_group.? Can this different elections of the tc_grps affect the final PMF profile? Thanks in advance, best regards, Facundo -- View this message in context: http://gromacs.5086.n6.nabble.com/small-tc-group-tp5001927p5001937.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
