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.