Dear GROMACS users, I followed the Umbrella Sampling tutorial to run a simple simulation of pulling polymer chain from the surface of micelle. I used position restraints for the initial equilibration, however I realized a typo in the define=-DPOSRES mdp files for pulling, US_NPT and US_MD simulations later during analysis. The simulations ran normally and the PMF plots look accurate. However, I realized that position restraints were not applied only after looking at the log files and position restraints energy values were missing. The umbrella sampling MD simulation was for 2 ns only and I checked the pullx-umbrella.xvg files and the COM fluctuations are not that bad considering its only a short time for convergence.
Can anyone comment on how not using position restraints would effect the result otherwise? Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/Umbrella-sampling-position-restraints-tp5010405.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
