Hello,<br><br>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:<br>
1) Generate a trajectory of configurations along the reaction coordinate.<br>2) Use the difference configurations as starting points for independent simulations in sampling window.<br>3) Use umbrella sampling to constrain in window.<br>
4) Use g_wham to construct PMF<br><br>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.<br>
<br>I really appreciate the help. Nobody in my lab has done this before, and I am feeling pretty unsure of myself.<br><br>Thanks.<br>