Lanyuan Lu wrote: > Hi Mark, > Thanks for your reply. Yes, I did save velocities in the same frequency > as positions. And the length of two compared trajectories are exactly > the same. I think I've figured it out and I did looked at the average > values as the output of the g_energy. It seems the number 545.384 from > the original MD edr file is incorrect. I opened the xvg file in xmgrace > and found the average pressure should be 1153.22, which is close to the > rerun result. I used the command "g_energy -f *.edr -o *.xvg" to dump > the pressure from two edr files and found both of the two xvg files have > time from 0 ps to 200 ps with 201 frames. I also found for each time > step the pressure values are close for the two files. Therefore, I don't > understand why I got the incorrect average pressure from the original > edr output, while the rerun output was correct. Another test I did was > to type "g_energy -f *.edr -o *.xvg -b 100" to get the last 100 ps > results. And this time the average number from the original edr file is > still incorrect. However, just as in the whole 200 ps case, I can get > the right number if I manually calculate the average from the xvg file. > Lanyuan
Hence... >> Did your primary mdrun include an >> equilibration period that the rerun did not? See appendix C.2. The averages reported by g_energy are not necessarily the averages of the data in the file. You can see whether this is happening by comparing a gmxdump of the two .edr files, or using the gmxcheck facility for comparing them. Assuming that your original mdrun was pre-equilibrated, I expect you will see the partial sums are different at each step - and the first one in particular. Mark _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
