Hello, I am a new Gromacs user, and I could really use some clarification about the pull code. I am interested in creating the PMF for Na+ and I- in the presence of THF. I saw a previous posting that the best way to go about creating the PMF is: 1) Generate a trajectory of configurations along the reaction coordinate. 2) Use the difference configurations as starting points for independent simulations in sampling window. 3) Use umbrella sampling to constrain in window. 4) Use g_wham to construct PMF
This is how I am interpreting the instructions, but could you please let me know if I am correct in my assumptions? First I create a couple of unique starting configurations, with Na+ and I- separated by specific distances. Once that has been done, I take one such configuration and turn on the options under com_pulling (especially pull_geometry = umbrella) in the .mdp file. I let this run for some amount of time, and end up with a pullx.xvg and a pullf.xvg file. I do this with the other configurations as well. Once that has been done, I take all of these .xvg and .tpr files and create a .dat file, which can be used with g_wham to construct the PMF. I really appreciate the help. Nobody in my lab has done this before, and I am feeling pretty unsure of myself. Thanks.
-- 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
