Hi I am trying to generate an equilibrated box of 216 TFE molecules.To generate the 216 TFE molecule box i performed following steps:
1) I got the tfe.gro file and created a cubic box of edge length = 0.516 nm containing 1 TFE molecule (at its center), using the following command: >> editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516 I chose this length because in the tfe.gro file dimensions of the TFE molecule are 0.516 0.516 0.516. 2) Then using genconf command i replicated the box to get a bigger box with 216 TFE molecules using the following command: >> genconf -f tfe_box.gro -o out.gro -rot -nbox 6 3) Energy minimization was done using STEEPEST descent 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns NPT (300K, 1atm) equilibration. After doing all these steps still I obtain a positive a potentail energy. I get positive potential energy of the system (2.45+E04 kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive total energy of the system. My question is whether obtaining positive potential energy indicate some error in my TFE solvent box ? Is it because of large Fluorine atoms of TFE ? Does it mean its not properly equilibrated ? What can I do to equilibrate it? Thanks. Harpreet -- 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
