[gmx-users] Acetone parameters and transferability question

Justin Lemkul jalemkul at vt.edu
Sun Oct 12 03:47:00 CEST 2014

On 10/10/14 6:16 PM, Ioanna Styliari wrote:
> Dear gmx users,
> I am using Gromacs 4.6.5 to simulate some amphiphilic diblock copolymers (for
> which I have created the .rtp files) in acetone and water mixtures. I am
> using the GROMOS53a6 force field.
> At the beginning I used the Automated Topology Builder to get the acetone
> files and parameters but it appears that their acetone doesn't diffuse
> properly with water. As I was going through the literature I found that there
> isn't a "good" acetone model apart from one (PAC - see reference 1 below)
> which has been modified for the CHARMM force field. In order to test that and
> also other different models (for OPLS as well) and how they mix with water I
> transferred all their parameters (bonds angles, charges, created new atom
> types with appropriate LJ parameters) for the 53a6 force field, based on the
> fact that when Geerke et all did the 53a6ff evaluation (see reference 2) they
> used the two OPLS acetone models for their calculations.
> I am worried whether this transfer is wrong. Could you please comment on it
> and if you think it is, suggest what else can be done?

Generally, converting from one force field to another is not a reasonable 
approach, because the parametrization methods are different and in some cases, 
things like combination rules are different between force fields.

What exactly was wrong the the parameters from ATB?  Was the diffusion constant 
wrong?  Note that such properties are not target data in Gromos96 
parametrization, so it would not surprise me if they didn't come out right.  The 
parametrization methods largely revolve around targeting thermodynamic 
properties.  Even common water models like TIP3P and SPC (against which Gromos96 
was parametrized) diffuse 2-3x too fast.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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