[gmx-users] Atomistic Simulation

Justin Lemkul jalemkul at vt.edu
Tue Dec 3 13:58:50 CET 2013

On 12/3/13 6:17 AM, Hardy, Adam wrote:
> I've just started doing atomistic simulations over the last few weeks as well and can share what I've learned so far.
> I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use it. ATB generates the pdb and itp files for you. There are a lot of molecules already on there or you can submit you're own using a java script molecule builder.
> There may well be other ways to do this but I haven't found them yet.

There are many other sources of parameters for simple molecules like these.

1. http://virtualchemistry.org/
2. https://www.paramchem.org/
3. AmberTools can be used to build (using xLeap) and create topologies 
(antechamber) for just about anything under GAFF

There are plenty of other sources.  The most important choice is constructing a 
model that accurately reproduces quantities of interest.  It may take several 
attempts using several force fields to find the right one, or you may have to 
derive your own model from scratch if none of the existing ones is sufficient.

> On 3 Dec 2013 10:14, panzu <sergio.panzuela at estudiante.uam.es> wrote:
>    Hello to everybody,
> I am new in atomistic simulations and a have some doubts about how to do it.
> I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane.
> My  questions are, ¿Where do I get the pdb files of these molecules
> from? and ¿How do I know which force field I should choose in pdb2gmx
> in order to make the itp file?

You don't need pdb2gmx at all here.  The topology should be manually 
constructed; pdb2gmx is not useful in cases like these.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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