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

[Justin Lemkul]

On 12/28/15 1:40 AM, Man Hoang Viet wrote:
> Hi,
>
>> Date: Sun, 27 Dec 2015 16:03:50 -0500
>> From: Justin Lemkul <jalemkul at vt.edu>
>
>> 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
>
> My simulation for energy calculation is steep minimization with nsteps=0.

This is the wrong way to calculate a single point energy.

http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

Note the last paragraph.

-Justin

> This simulation gives energy information of the initial structures which
> are the same in both AMBER and GROMACS simulation.
> I can't not produce exact conformations as The Sorin done group for
> testing without their code, however I do test for the initial structures
> generated by Leap in AMBER by the same way I did for my previous tests.
> This test result is shown in below table:
> Error(%) & ff99   & ff99SB  & ff12SB  & ff14SB
> BOND     & 0.001  &  0.001  &  0.001  &  0.001
> ANGLE    & 0.000  &  0.000  &  0.000  &  0.000
> DIHEDRAL & 0.000  &  0.000  &  0.000  &  0.000
> 1-4vdW   & 0.000  &  0.000  &  0.000  &  0.000
> 1-4QQ    & 0.000  &  0.000  &  0.000  &  0.000
> vdW      & 0.000  &  0.000  &  0.000  &  0.000
> QQ       & 0.002  &  0.002  &  0.002  &  0.002
> Epot     & 0.005  &  0.004  &  0.004  &  0.004
>
> In my view, it is not clear what cause the dihedral energy difference. My
> test assessment, the force field implementations (ff99, ff99SB, ff12SB and
> ff14SB) and the different  dihedral energy calculations between GROMACS
> and AMBER are all possible for making the problem. I will try to figure
> out this issue.
>
>
> Viet Man,
> Postdoctoral Reseach Scholar
> Department of Physics, NCSU
>

-- 
==================================================

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

==================================================