Hallo all together, I am working on a system of a small peptide solvated in CHCl3. I want to obtain the forces on the peptide atoms induced by the solvent. For this I used the rerun option of mdrun_d. I did it now in two ways: 1st: using trjconv to get the pure peptide trajectory. When using the rerun option with no special configurations of the .mdp file. If the obtained force are pair additive I should get the wanted result if I subtract from the forces of the original trajectory the rerun forces. 2nd: using the original trajectory and changing the options of the .mdp file as follows: energygrps = Protein SOL energygrp_excl = Protein Protein SOL SOL and changing the coulomb type to Cut-off because of the separation problem using PME.
Comparing this two results I realize that they are totally different. There is no correlation to detect between this two. I am wondering now which way to go to get the correct answer for my question. I probably just do not understand the energygrps and energygrp_excl option right. Using rerun with the same trajectory and the same .mdp option except changing PME to Cut-off gives the same result as the original trajectory or at least up to the last 3 decimal places of a double value. I would be really happy if someone can help me Thanks a lot Sebastian -- 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
