[gmx-users] g_mdmat

Dear Gromacs user, I'm trying to calculate de distances between residues in a trajectory with g_mdmat and I'm coming across a problem while trying to restrict only to a smaller number of residues providing an index file. in fact what I get is a matrix as big as if I use all the residues, and the

[gmx-users] g_mdmat distance matrices

Dear gmx users, I used g_mdmat and have got a distance matrices in .xpm format. Now I want to compare two matrices: for a protein var1 and for protein var2 and create one output file with this compare. How can I do it? If there is no such function in gromacs, how can I convert .xpm format to

[gmx-users] g_mdmat

Dear friends, I have used g_mdmat g_mdmat -f traj.xtc -s md.tpr -mean dm.xpm -frames dmf.xpm -no num.xvg I got dm.xpm graph which shows mean of whole simulation residue contacts. How to get information about the particular residue are n contact? I mean to say, Is there any tool to give list of

[gmx-users] g_mdmat

Hello list, does g_mdmat ouput the standard deviation that goes along with the mean.xpm file? Thank you. -Rob _ ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] g_mdmat question

Dear gmx users, I have a question about g_mdmat, related to a question I posed earlier. I know a bit more now. When I run the command on a trajectory in pdb format, either using -b and -e to specify which string of frames to average over, or just leaving -b, -e unspecified, I get a contact