There was no water. Version 4.5.5. Single precision. This is what I ran: pdb2gmx -f 1.pdb -p g1 -o g1 grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.19780e+02 kJ/mol
grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.15997e+02 kJ/mol The mdp file: integrator = md nsteps = 0 nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy = 1 nstxtcout = 0 nstlist = 0 ns_type = simple pbc = no rlist = 0 rcoulomb = 0 rvdw = 0 gen_vel = no unconstrained-start = yes lincs-warnangle = 30 The pdb file : HETATM 1 1HH3 ACE 1 -1.449 0.109 -0.581 H HETATM 2 CH3 ACE 1 -2.101 -0.268 0.202 C HETATM 3 2HH3 ACE 1 -1.708 0.090 1.151 H HETATM 4 3HH3 ACE 1 -2.109 -1.350 0.189 H HETATM 5 C ACE 1 -3.491 0.269 0.000 C HETATM 6 O ACE 1 -4.453 -0.401 -0.152 O ATOM 7 N GLY 2 -3.601 1.734 0.000 N ATOM 8 H GLY 2 -3.039 2.278 -0.623 H ATOM 9 CA GLY 2 -4.525 2.391 0.903 C ATOM 10 HA1 GLY 2 -5.539 2.051 0.696 H ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 H ATOM 12 C GLY 2 -4.461 3.901 0.720 C ATOM 13 O GLY 2 -3.677 4.400 -0.128 O HETATM 14 N NME 3 -5.316 4.776 1.535 N HETATM 15 H NME 3 -6.182 4.876 1.044 H HETATM 16 CH3 NME 3 -4.685 6.072 1.731 C HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 H HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 H HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 H END *In reply to chris.neale at utoronto.ca:* It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters?
-- 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