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 <mhv...@ifpan.edu.pl> wrote: > Hi Justin, > > > Date: Mon, 28 Dec 2015 08:18:45 -0500 > > From: Justin Lemkul <jalem...@vt.edu> > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Update Amber force fields, ff12SB abd ff14SB > > gromacs implementation testing > > Message-ID: <568136b5.5090...@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 <jalem...@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 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.