[gmx-users] Update Amber force fields, ff12SB abd ff14SB gromacs implementation testing

Man Hoang Viet mhviet at ifpan.edu.pl
Sun Dec 27 21:56:25 CET 2015


> 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:
>> http://www.gromacs.org/@api/deki/files/252/=ffA2G_test.pdf
>> and the test data set updated at:
>> http://www.gromacs.org/@api/deki/files/253/=FF12SB_FF14SB_GROMACS_TEST.tar.bz2
> 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.
> -Justin

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.

Viet Man,
Postdoctoral Research Scholar,
Department of Physics, NCSU.

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