[gmx-users] Restrain specific lipid residues

Justin Lemkul jalemkul at vt.edu
Tue Sep 25 23:16:50 CEST 2012

On 9/25/12 5:14 PM, Katrina Lexa wrote:
> 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).

Restraints can only be applied per [molecultype], so no, there is no way to have 
a global lipid topology and individual restraint files for individual molecules. 
  It is possible to reduce the complexity a bit by defining the 33 restrained 
lipids as one [moleculetype], though they would have to be consecutive in your 
coordinate file as well, which may require manual reorganization.

> 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).

Glad to hear there's at least one problem solved :)



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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