[gmx-users] MD simulation with glycerol
Justin A. Lemkul
jalemkul at vt.edu
Mon Feb 22 16:33:49 CET 2010
politr at huji.ac.il wrote:
> Hi Justin,
> one more question. Do yuo think I should use opls_174 or opls _175 for a
> middle C of glycerol?
> in atp file opls_174 12.01100 ; C(HROH): triols
> opls_175 12.01100 ; C(R2OH): triols
> both of them seems to be for triols and i can't understand which one is
> suitable for this carbon. Do you have some suggestion?
Not really. Both have identical LJ parameters (see ffoplsaanb.itp); I don't
know what the charge in the nb.itp file pertains to, but you can set whatever
charge you think appropriate in the topology manually.
> Thank you again.
> 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
>>> 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
>>> This message was sent using IMP, the Internet Messaging Program.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users