[gmx-users] Update Amber force fields, ff12SB abd ff14SB gromacs implementation testing
jalemkul at vt.edu
Sun Dec 27 22:04:03 CET 2015
On 12/27/15 3:56 PM, Man Hoang Viet wrote:
>> Date: Fri, 25 Dec 2015 20:24:41 -0500
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Update Amber force fields, ff12SB abd ff14SB
>> gromacs implementation testing
>> Message-ID: <567DEC59.3040101 at vt.edu>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>> On 12/24/15 5:04 AM, Man Hoang Viet wrote:
>>> Dear GROMACS users,
>>> I have completed the test for the Amber force fields, ff12SB and ff14SB,
>>> implementation into GROMACS.
>>> The test report is updated at:
>>> and the test data set updated at:
>> The dihedral error is rather large, and specific to the protein
>> parameters. This
>> suggests there is something being calculated somewhat differently. Can
>> you use
>> simple single-point energies to identify the source of this problem?
>> Errors in
>> dihedrals can impact sampling quite a bit.
> I have just done test for amber99 force field and the result is similar to
> other amber force fields (see in below link).
> The table 3 shows the dihedral energy differences of small residues such
> as GLY and ALA are significant larger than other ones. I think the smaller
> residues the more sampling in the give simulation time (1ns), therefore
> the dihedral phase space of the small amino acids are broader than bigger
> Maybe, the sampling conformations is the main reason making my test result
> on dihedral energy is a bit different with the one fro Prof. Eric J.
> Sorin. (with the same force field amber99).
> I will try to find out the sources that cause dihedral energy differences
> between AMBER and GROAMCS in my test.
The energy of the same configuration in both AMBER and GROMACS should be the
same if the force field implementation is equivalent. You don't need to run
simulations, extract conformations, etc. to get this. Take one coordinate file,
calculate its energy in each program, and report the result. The Sorin group
did a slightly more complex version of this, by testing several different
coordinate perturbations (the reason for which is explained on their website),
but the for the purpose of troubleshooting, a single configuration should do
initially. It's really quite straightforward. If the same coordinates produce
different energies, there is a fundamental problem in the force field
implementation. If the problem is shared among Gly and other amino acids, this
implies a backbone problem, which is very troubling, but the fact that you can't
reproduce the ff99 result means you're likely doing something incorrectly in
your assessment. Be sure you're doing single-point energy calculations
correctly using mdrun -rerun.
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
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