Hi Chris Sorry I sent my e-mail just prior to receiving yours? Is it any clearer?
Gavin [email protected] wrote: > The pullx file should contain everything that you need. dX,dY,dZ *are* > the components of the distances between the two groups. > > I still don't understand your question (perhaps you could give us a > worked example with real data?), but if you just want the COM > distance, then try this: > > cat pullx.xvg |awk '{print sqrt($1,$5*$5+$6*$6+$7*$7)}' > my.dist > > of vourse, what you need depends on your pull code options, but this > should give you a start. Combine this with VMD and you should be able > to figure out what you need. > > Chris. > > -- original message -- > > Hi all > > In hindsight I think the question I posted yesterday may have been a > little naive. To rephrase it - If the pullx.xvg files contain X Y Z dX > dY dZ, (because pull_dim = Y Y Y), does the g_wham programme calculate > the centre of mass distances to use in the histogram i.e. Will the first > column in the histo.xvg file be the centre of mass distances (the > modulus of the three vector components)? > > Cheers > > Gavin > > Gavin Melaugh wrote: >> Hi All >> >> I have generated a series of configurations for two molecules >> approaching along the z axis. I am now going to run umbrella sampling of >> these configurations at a fixed distance (XYZ) in order to calculate the >> PMF. I understand that the output of the pulling code gives a pullx.xvg >> file which serves as the input to g_wham. I notice that this file does >> not contain the distances between the COMs of the two molecules. Is >> there anyway of generating a file that contains such information >> directly form mdrun or do I have to run g_dist for every trajectory >> generated. If this is the case can the output from g_dist serve as the >> input for g_wham (like pullx.xvg). >> >> Cheers >> >> Gavin > > -- 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
