[gmx-users] MD simulation with glycerol

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 22 12:55:41 CET 2010

politr at huji.ac.il wrote:
> Dear Justin,
> Thank you for a quick replay. Do you know if there are some atom types, 
> charges, parameters, etc that incorporates sugar and alcohol potentials 
> determined by Jorgesen "OPLS all atom force field for carbohydrates"?

No clue.  Have a look through the .atp file to see; there are hundreds of atom 
types available.  If the ones you need haven't been implemented, you can easily 
add a new [atomtypes] section to your handmade topology.


> Regina
> Justin A. Lemkul wrote:
>> 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 :)
>> -Justin
>>> Thank you a lot for your help
>>> Regina
>>> ----------------------------------------------------------------
>>> This message was sent using IMP, the Internet Messaging Program.


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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