[gmx-users] MD simulation with glycerol

politr at fh.huji.ac.il politr at fh.huji.ac.il
Sun Feb 21 22:29:21 CET 2010

Dear Gromacs users,
I'm completely new in Gromacs. I would like to perform a simulation of  
a peptide in water (SPCE) in glycerol presence using OPLS-AA. I want  
to know where can I find the parameter and topology file in order to  
create a solvation box that includes glycerol. Should I construct  
glycerol from some building blocks? If yes what files do I need to  
update?  A similar message was posted once on the Gromacs mailing list  
but there was no answer on how to do it. I found a paper "OPLS all  
atom force field for carbohydrates" and a couple of papers that cite  
this paper so maybe the parameters from this paper are already  
implemented to Gromacs. In addition, I used NAMD to perform this  
simulation so I have a pdb file that contains my peptide dissolved in  
water box (TIP3P)  with glycerol molecules presented as well.  Can I  
use this file in some way  to generate files for simulation  in  
Gromacs.  If yes, what should I change and how should I proceed in  
order to perform the simulation? I'm using Gromacs VERSION 4.0.3.
Thank you a lot for your help

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