[gmx-users] Probability contact map from g_mdmat

Dear All, I was playing around with g_mdmat to try and obtain a probability contact plot instead of a mean plot or a frame dump, where it would count the number of times a distance would occur between a range eg. 0-0.4nm. This way the map would show the contact, as well as the propensity to form th

Re: [gmx-users] DSSP error

May be the directory you are working in is read only, as Justin mentioned this could be a permissions issue. As an example the super computer that I use, cannot write anything in the home directory, therefore all simulations and analysis are done in scratch. Ali -- gmx-users mailing listgmx-

Re: [gmx-users] Parallel do_dssp analysis over mpi?

Thank you Justin, Mark and Erik for your help. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the li

[gmx-users] Parallel do_dssp analysis over mpi?

Dear All, I have a trajectory of 100ns and have been trying to analyze it using dssp program. I guess this question also goes for other analysis programs like g_rama, g_rdf and what not. Since the trajectory is big, it takes hours to analyze with do_dssp.. infact 48 hours. I have been able to anal

Re: [gmx-users] Dihedral energy map along two eigenvectors to actual conformations

Found the answer, thanks to personal communication by Dr. Yuguang Mu. Here it is for anyone interested. Each point on the energy landscape corresponds to a time. This time can be tracked simply by using g_anaeig and using -proj to assign a file name and -first, -last to assign eigenvectors of inte

Re: [gmx-users] Dihedral energy map along two eigenvectors to actual conformations

> > Yes I have been using the how-to for making the energy landscape. Now I > just need to go backwards. > > Ali Naqvi wrote: > > Hi all, > > I have been following the method outlined by Yuguang Mu to generate the > > energy landscape along two eigenvectors. Ther

[gmx-users] Dihedral energy map along two eigenvectors to actual conformations

Hi all, I have been following the method outlined by Yuguang Mu to generate the energy landscape along two eigenvectors. There are four minima that I wish to explore. I can determine the points along the vectors that correspond to the conformation, but am unsure of how to use those to obtain the co

[gmx-users] Re: Joining groups for simultaneous analysis in DSSP (Justin A. Lemkul)

Genius! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it t

[gmx-users] Joining groups for simultaneous analysis in DSSP

Hi all, I have a 25 amino acid peptide that contains 4 phosphoserines. The forcefield that I have been using is the ff43ap which was modified to include these groups. So during pdb2gmx I have the rtp and itp files for the forcefield in the folder in order for the software to find the appropriate ch