[gmx-users] MD simulation with glycerol

Justin A. Lemkul jalemkul at vt.edu
Sun Feb 21 23:07:42 CET 2010

politr at fh.huji.ac.il wrote:
> 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 

You don't need to update any files in order to create a new topology using 
existing building blocks - make use of the .atp, .rtp, nb.itp, and bon.itp files 
to choose your atom types, charges, bonded parameters, etc.

> 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 

If you already have proper parameters for glycerol (since you've simulated it 
with NAMD), then likely much of the hard work is already done.  Chapter 5 of the 
manual is your friend here.  The NAMD topology can't be used directly, but with 
the help of your favorite text editor, constructing the Gromacs-formatted 
topology should not be very difficult.  The only key thing about using 
pre-existing building blocks or whatever chemical intuition is that you can 
somehow validate these parameters, ideally following the methodology that has 
been published.

> Gromacs VERSION 4.0.3.

Unless you've got a compelling reason to use a version of the software that is 
over a year old (continuity with previous work, etc), upgrade to 4.0.7 to enjoy 
the newest features and bug fixes :)


> Thank you a lot for your help
> Regina
> ----------------------------------------------------------------
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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