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

[Mark Abraham]

Hi,

You can only get the total dihedral energy of all the dihedrals in your
system. You can use e.g. gmx convert-tpr to make subsets of your .tpr for
diagnosis, however.

And you need to report some units on your energy differences ;-)

Mark

On Tue, Dec 29, 2015 at 6:41 PM Man Hoang Viet <mhviet at ifpan.edu.pl> wrote:

> Hi Justin,
>
> > Date: Mon, 28 Dec 2015 08:18:45 -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: <568136B5.5090109 at vt.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > 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.
>
> Thank you very much for the information. I have corrected my test as below
> commands:
> grompp_s  -f eqtest.mdp -p  v.top -c  test.pdb -o  test.tpr
> mdrun_s -nt 1 -s test.tpr -rerun test.pdb -g test.log
> Then the energy information were taken from test.log
>
> eqtest.mdp:
> ##############
> integrator          =  md
> emtol               =  100.0
> emstep              =  0.005
> dt                  =  0.000001    ; ps !
> nsteps              =  1  ; total 100 ps
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist         = 10
> ns_type         = grid
> rlist           = 1.0
> coulombtype     = cut-off
> rcoulomb        = 1.0
> vdwtype         = cut-off
> rvdw            = 1.0
> ewald_rtol      = 1e-5
> ###############
>
> However, the result is still the same as what I reported. Could you please
> tell me other way to directly calculate diheral engery by GROMACS from a
> give structure (or dihedral)? Till now, I do not think my test assessment
> causes the difference of the dihedral energies.
>
>
> Viet Man,
> Postdoctoral Research Scholar,
> Department of Physics, NCSU
>
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