I've refined the charge distribution. nr type resnr resid atom cgnr charge- prodrg (NEW) mass 1 OA 1 F09 OAD 1 -0.117 (-0.596) 15.9994 2 H 1 F09 HAD 1 0.027 (+0.469) 1.0080 3 C 1 F09 CAC 1 0.078 (+0.274) 12.0110 4 CR1 1 F09 CAF 1 -0.005 (-0.390) 12.0110 5 HC 1 F09 HAF 1 0.014 (+0.195) 1.0080 6 C 1 F09 CAH 1 -0.014 (+0.104) 12.0110 7 CR1 1 F09 CAI 1 -0.006 (-0.197) 12.0110 8 HC 1 F09 HAI 1 0.014 (+0.140) 1.0080 9 CR1 1 F09 CAK 1 -0.005 (-0.139) 12.0110 10 HC 1 F09 HAK 1 0.014 (+0.139) 1.0080 11 CR1 1 F09 CAL 2 -0.006 (-0.139) 12.0110 12 HC 1 F09 HAL 2 0.014 (+0.139) 1.0080 13 CR1 1 F09 CAJ 2 -0.005 (-0.197) 12.0110 14 HC 1 F09 HAJ 2 0.014 (+0.140) 1.0080 15 C 1 F09 CAG 2 -0.014 (+0.104) 12.0110 16 CR1 1 F09 CAA 2 -0.005 (-0.390) 12.0110 17 HC 1 F09 HAA 2 0.013 (+0.195) 1.0080 18 C 1 F09 CAB 2 0.078 (+0.274) 12.0110 19 OA 1 F09 OAE 2 -0.116 (-0.594) 15.9994 20 H 1 F09 HAE 2 0.027 (+0.469) 1.0080 The ones in the bracket are the new charges applied. These are from the Automated Topology Builder which does the QM calculations. They seemed more appropriate as they match with the ones on p-cresol in the paper. I did not modify the bond parameters from PRODRG as suggested by the paper. The potential energy has reduced and is arnd 1.5e+04 but is still positive. Can I get some help with this? Thank you for all the help in advance. :)
Satish Kamath IISc Bangalore -- View this message in context: http://gromacs.5086.n6.nabble.com/Positive-Potential-Energy-after-equilibration-tp4998327p4998362.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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