[gmx-users] Re: Density question

[Justin A. Lemkul]

teklebrh at ualberta.ca wrote:
> Dear Gromacs Users,
> 
> I run an MD simulation of a pure solvent and found out that the density 
> of the solvent deviated a little bit from the actual experimental data.
> 
> MD density is 880g/ml and the experimental data is 866g/ml. Is this 
> reasonable for toluene solvent molecules.
> 
> I have a hard time of lowering the density to the experimental value. I 
> am using ff53a6 gromos force field with rlist=rvwd=rcoulomb=0.9nm.
> 
> Is there any advice on this or it is OK.
> 

I'd say a 1.6% difference is quite outstanding.  If you're using the standard 
parameters for this force field (i.e., Phe side chain), then that's probably the 
best you can do, since that's how the force field was derived in the first place.

-Justin

> Thank you
> 
> Rob
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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