Hello, Thanks for the reply. I made another even more simple test. I just would like to understand what is going on inside the energy calculation. I have an ALA system. This is the topology file for the bond:
[ bonds ] ; ai aj funct r k 1 2 1 1.0100e-01 3.6317e+05 3 4 1 1.0900e-01 2.8451e+05 5 6 1 1.0900e-01 2.8451e+05 5 7 1 1.0900e-01 2.8451e+05 5 8 1 1.0900e-01 2.8451e+05 1 3 1 1.4490e-01 2.8200e+05 3 5 1 1.5260e-01 2.5941e+05 3 9 1 1.5220e-01 2.6527e+05 9 10 1 1.2290e-01 4.7698e+05 From here, I computed manually the bond energy which is : sum (ki*(r_i*r_i)) = 42536.87 (kj/mol) however, when I perform a rerun on the gro file ... this is the bond energy: 2.20074e-01 (kj/mol) What am I missing? Thanks G. ________________________________ From: David van der Spoel <sp...@xray.bmc.uu.se> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Thursday, August 8, 2013 2:40 AM Subject: Re: [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k On 2013-08-08 01:16, Golshan Hejazi wrote: > Hello, > > I have performed quit a lot of tests and I have some question: > I have an amber.crd and amber.top files ... I perform a single step energy > calculation with amber , gromacs and cp2k. in all of them I am using amber > force field but the point is that in cp2k and amber, I am reading crd and top > file directly while in gromacs, i need to convert them to gromacs format. > > I performed this test for a simple ace-ala-nme system. Lets talk only about > the BOND, ANGLE and TORSION energies which are the same in all of these > packages. these energy components output are identical in amber and cp2k. > However, there is a big difference between them and gromacs: > > cp2k, amber ... BOND= 0.0206 (kcal/mol) ANGLE=0.3620 (kcal/mol) > TORSION=8.1071 (kcal/mol) > gromacs .... BOND=0.14044 (kcal/mol) ANGLE=0.3780 (kcal/mol) > TORSION=9.74190 (kcal/mol) > > The other terms are also different. But lets focus on these because they are > the same in all these packages. > > Now, how did i convert the crd and top file to gromacs fromat? > > 1- I tried amb2gmx perl script > 2- I used ambpdb of amber to generate a pdb file and then pdb2gmx of gromacs > to generate the top and gro file for gromacs > > BOTH of these ways gives different results from each other and also from cp2k > and amber! > I would really appreciate any help about this problem ... it seems to me > there is a bug in amber to gmx file convertors?! > it looks like some kind of rounding error, pdb file have limited precision. the force constants you can check yourself. > Thanks > Golshan > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
