[gmx-users] Re: small tc-group

[fciocco]

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



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