Dear Chris and Justin I ran a simulation for two water molecules (100 ns). It only took 5 minutes. Firstly I ran the simulation with ref distance 2.35 nm, genvel =yes, and gen temp =600 (using Nose Hoover). This produced a histogram with one main peak. I then took the final configuration from that simulation and ran the simulation again for the exact same duration and parameters etc, with the only exception that I set gen_vel = no. The resulting histogram did indeed have two main peaks. I am now currently running the simulation of my two cage molecules using berensden thermostat to see if there is a difference.
Many Thanks Gavin chris.ne...@utoronto.ca wrote: > Dear Gavin: > > What happens if you replace your reference group by a single water > molecule and your pulled group by a single water molecule and run the > 2.35 nm simulation again. Do you get the same two-peaked histogram? > What about if you use a system with a single water for the reference > and your regular pulled group? > > You should not need to run 100 ns to get an idea about the shape of > that histogram so it should be a quick test. This is usually how I > figure things out -- see how much I can reduce the complexity and > maintain the problem. > > Chris. > > > -- original message -- > > Hi Chris > > I have generated a histogram from the my.data file and i get a histogram > with the exact same profile as that generated from g_wham. Also on > comparison of the dx, dy, dz values in the g_dist file with the vaules > in the pullx.xvg file I notice that the magnitudes of the vectors are > identical but their signs are opposite. e.g. > g_dist file > -2.2756047 -0.0369981 0.3126130 > > pullx.xvg file > 2.2756 0.036998 -0.312613 > > Cheers > > Gavin > > Please note that there is a significantly more interaction between the > molecules below 2 nm whereas above they interact very weakly (from > viewing the trajectories) > > > -- 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/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/mailing_lists/users.php
