lammps lammps wrote: > Hi everyone, > I use umbrella sample and g_wham to get potential of mean force. > However, I also want to compute the mean force. How can I deal with > this? Can I get it through calculating the average of data in > pullf.xvg file?
In principle, yes. But note that the position of the particle fluctuates within the umbrella window during your simulation. A more well-defined force would be computed by using pull = constraint and then by averaging the pullf.xvg output. In theory, you should then get the same PMF by either integrating the mean force or by using wham on the umbrella ouput. Best, Jochen > Thanks in advance. > Wende > ------------------ > ;spring point is equal to ref_group0+pull_init+time*pull_rate*pull_vec， > pull = Umbrella ;umbrella,constraint > pull_geometry = Distance ;distance ,direction,cylinder,position > pull_dim = Y Y Y > pull_group0 = DEN1 > pull_group1 = DEN2 > pull_nstxout = 500 > pull_nstfout = 50 > pull_init1 = 5.7 > pull_k1 = 1000 > ------------------- > # This file was created Thu Feb 4 00:51:24 2010 > # by the following command: > # mdrun_mpi -rdd 1.4 -s npt.tpr -c npt.gro > # > # mdrun_mpi is part of G R O M A C S: > # > # Groningen Machine for Chemical Simulation > # > @ title "Pull force" > @ xaxis label "Time (ps)" > @ yaxis label "Force (kJ/mol/nm)" > @TYPE xy > 0.0000 -28.8555 > 1.6000 -19.2897 > 3.2000 -18.59 > 4.8000 -20.7866 > 6.4000 -26.1605 > 8.0000 -42.8572 > 9.6000 -50.7524 > 11.2000 -73.9647 > 12.8000 -74.2521 > 14.4000 -102.284 > 16.0000 -96.5184 > > -- > wende -- --------------------------------------------------- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell & Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --------------------------------------------------- -- 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
