[gmx-users] mismatch between energies of sequential minimization runs
Hi, I am running 2 sequential minimizations with the same mdp file. As expected the second minimization stops in step zero and the resulting structures of the 2 minimization runs are identical (RMSD=0.0). But, the energies of the last step of the first minimization (step 14) and the zero step of the second minimization are not identical (see below). What could be the reason for this mismatch? Thanks, Efrat First minimization: Step Time Lambda 14 14.00.0 Energies (kJ/mol) Bond Angle Ryckaert-Bell. Improper Dih. LJ-14 1.95260e+011.32951e+021.29144e+023.99233e-014.69282e+01 Coulomb-14LJ (SR) Coulomb (SR) Potential Pressure (bar) -3.24612e+03 -3.33371e+014.24793e+031.29742e+030.0e+00 Second minimization: Step Time Lambda 00.00.0 Energies (kJ/mol) Bond Angle Ryckaert-Bell. Improper Dih. LJ-14 2.24603e+011.31903e+021.29221e+023.98797e-014.61009e+01 Coulomb-14LJ (SR) Coulomb (SR) Potential Pressure (bar) -3.24585e+03 -3.32600e+014.24778e+031.29876e+030.0e+00 -- gmx-users mailing listgmx-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] detailed energies per interaction
Hi, How can I get detailed energies per interaction (that is bonding and non-bonding terms for each pair/threesome/foursome of atoms) in Gromacs? Thanks, Efrat-- gmx-users mailing listgmx-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] OPLS-AA topologies for ATP
Hi, Does anyone have OPLS-AA topologies for ATP? Thanks, Efrat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Gromacs test sets
Hi everyone, I have just installed Gromacs (version 4.0.7), run the test sets (gmxtest-4.0.4) and got few failures. I looked at the relevant 'checkpot.out' and 'checkvir.out' files as suggested in previous messages. For the 'complex' tests I got no differences in the 'checkpot.out', only in the 'checkvir.out'. Some of the differences in 'checkvir.out' are quite large (see below example for water). For the 'kernel' tests I get differences both in 'checkpot.out' and in 'checkvir.out' and the differences are significant (see below example for kernel020). - Should I check any other files? - What should I do when the differences are significant? (I just installed gromacs with no errors) Thanks for your help, Efrat ___ complex/water/checkpot.out: There are 31 terms in the energy files There are 3 terms to compare in the energy files Files read succesfully _ complex/water/checkvir.out: Pressure (bar) step 50: 46893.3, step 50:44899 Vir-XX step 50: -6211.69, step 50: -6371.98 Vir-XY step 50: -2423.21, step 50: -1880.85 Vir-XZ step 50: 667.327, step 50: 381.986 Vir-YX step 50: -2422.22, step 50: -1880.17 Vir-YY step 50: -3194.86, step 50: -2649.86 Vir-YZ step 50: -2208.7, step 50: -2616.43 Vir-ZX step 50: 667.878, step 50: 382.404 Vir-ZY step 50: -2207.77, step 50: -2616.81 Vir-ZZ step 50: -1482.41, step 50: -752.677 _ _ kernel/kernel020/checkpot.out: LJ-14step 0: -63.1209, step 0: 6.50742 Potentialstep 0: -321.601, step 0: -251.972 _ _ kernel/kernel020/checkvir.out: LJ-14step 0: -63.1209, step 0: 6.50742 Potentialstep 0: -321.601, step 0: -251.972 Kinetic En. step 0: 15.0135, step 0: 29.0739 Total Energy step 0: -306.588, step 0: -222.898 Temperature step 0: 1.93226, step 0: 3.74185 Pressure (bar) step 0: -3095.37, step 0: -2497.79 Vir-XX step 0: 1127.45, step 0: 1075.85 Vir-XY step 0:63.524, step 0: 21.7761 Vir-XZ step 0: -264.813, step 0: -260.354 Vir-YX step 0: 63.5241, step 0: 21.777 Vir-YY step 0: 803.252, step 0: 581.702 Vir-ZX step 0: -264.813, step 0: -260.354 Vir-ZZ step 0: 321.207, step 0: 176.573 __-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
