[gmx-users] Restrain specific lipid residues

Katrina Lexa klexa at umich.edu
Tue Sep 25 23:14:13 CEST 2012

Hi everyone,

This is probably a very silly question, but if I want to restrain only certain lipid residues in my bilayer, based on their residue number, is there some other way to do this aside from just having an explicit residue-by-residue list of them & their topologies in my .top? I'm just using Tieleman's lipid parameters, so I cannot define the lipid residues to restrain following the popc.itp file, since it describes just the general topology for any POPC residue & tells me that my index is out of range, since the .top is in atom numbers & I'm trying to think in residue numbers. Does that sort of make sense? Out of my 165 residues, I want to strongly restrain only 33 of them, and then let the rest minimize (I'm trying to add onto an equilibrated box - at this point, it would have just been easier to start over from scratch, but I thought I would ask).

Also, thank you to Justin and Mark for your help with  hydrogen building in pdb2gmx - you were right, obviously, I was just not noticing the wrong atom type in my .h2b file (way back Aug 30th). 

Thank you for your help,


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