[gmx-users] How to examine our created topology

[Justin Lemkul]

On 2/15/15 9:39 AM, Faezeh Pousaneh wrote:
> Dear Justin,
>
> I simulate 2,6 dimethylpyridine (lutidine), C7H9N. I use ''gromos43a1''
> force field, and I have taken the charges on atoms from Gaussian software.
> By manipulating charges on the atoms I can get better agreement with
> experiment for the bulk, but then I loose it's aqueous properties (mixture
> of water-lutidine). How to overcome this problem?

Save yourself some time.  This compound is already available from ATB.

http://compbio.biosci.uq.edu.au/atb/molecule.py?molid=999&outputType=top&atbVersion=v2Top&ffVersion=54A7&format=GROMACS

They provide the experimental hydration free energy, which should (along with 
density) be a main point for validation of the model.

> Actually your suggestion ''but the relative contributions of these terms
> depend on the chemical nature of the molecule(s) involved'' is not clear
> for me.

It's inherently a generic statement, but it makes you think about the chemical 
nature of the problem.  Given I didn't know what your molecule was, I couldn't 
be specific.  If you have something with a bulky alkyl chain, you're probably 
not going to spend a lot of time on charges, because LJ will dominate. 
Conversely, something that is highly polar or charged would require some pretty 
good charges.  Ultimately, everything in a force field is a balance of all the 
contributions, so all can and should be tuned and scrutinized.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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