[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 that contact, relative to the covalent bonds shown on the diagonal. Anyway this would be more important to me than a means plot. I have searched the literature and this forum for "contact map gromacs" keywords without results except for a conversion from xpm to numbers script and a script that returns the various contacts g_mdmat found. Hence, I wanted to know if someone has done this on their own, so I won't reinvent. If not, I will modify the source and upload it to the user contribution page. Let me know. Cordially, Ali -- 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 to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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-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 to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 analyse only one set of 100ns and have 7 more trajectories. Is it possible to get it running in parallel to expedite the analysis? If so, which flags need to be appended? Cordially, Ali -- 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 to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 interest. This will generate a file that will show the values of the eigenvectors as a function of time. Subsequently, one can find the time at which the eigenvector values occurred by finding them as a point on the landscape and matching it to the eigenvectors vs time file. Hope my convoluted thinking made sense. :) Cheers, Ali -- 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 to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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. 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 corresponding pdb as was shown in the paper: > > > > Mu, et al. Energy Landscape of a Small Peptide Revealed by > > Dihedral Angle Principal Component Analysis, 2005. > > > > Any insight? > > > > Have you tried the dihedral PCA how-to? I don't know if it will give you > everything you want, but it's certainly a start. > > http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA > > -Justin > > > Cordially, > > Ali > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > -- > > -- > gmx-users mailing list > gmx-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! > > End of gmx-users Digest, Vol 78, Issue 212 > ** > -- 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 to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 corresponding pdb as was shown in the paper: Mu, et al. Energy Landscape of a Small Peptide Revealed by Dihedral Angle Principal Component Analysis, 2005. Any insight? Cordially, Ali -- 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 to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 charges. Anyway, simulation is all honkey dory but the problem is in DSSP analysis which separates the SEP from the protein. So the entire protein is 252 atoms but when I run the do_dssp program it is separated into two: Protein 208 atoms & SEP is 44 atoms I can run the dssp separately on the two groups, but since dssp uses information about adjacent sequence of amino acids, I would say separating the analysis in the SEP region 16-19 would be wrong as secondary structure would not be additive like lets say dihedral angles or rmsf. For results, in the SEP region I am getting the random coil (white as coloured by xpm2ps) which is equivalent to no secondary structure. Although I don't have a hard time believing this, just to be a devils advocate of my own results, I would like to process them together instead of separately. So my question is how to I join atoms into one group instead of having them separated? Cordially, Ali -- 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 to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
