[gmx-users] Convert to Sammon map

Dear All   I'd like to convert a gromacs RSMD matrix (xmp) to a Sammon map. Could you give me any suggestion?   Thanks-- 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/Se

[gmx-users] Cluster analysis

Dear all   Could you give me any suggestion about how I can interpretate output result of g_cluster? Is there a detailed tutorial?   Thanks-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Su

Re: [gmx-users] grompp error for CNT simulation

niaz poorgholami wrote: Dear gmx users, I am using gromacs 4.5.3 to simulate CNT in water. up to now I have done these things: 1. I used packmol to create my PDB file and the used editconf to change PDB to gro file. 2. I copied oplsaa.ff folder in my working directory 3. I added following l

[gmx-users] Half double pair list method in GROMACS [update]

Hi Sai I am also agree with Christ, your approach seems also correct to me. But don't to forget to test your change to be sure, by doing a single point energy test as it is said in the Christ's message. Good luck Stephane -

[gmx-users] output logfile

Hi,  It might be a very minor issue but I find in versions of gromacs 4.5.4, the output log file ( in verbose mode) writes the progress of the simulation in a single line ( unlike in previous gromacs 4.0.7 version) where it used to write the progress in a new lines. As a result, in gromacs4.5.4,

Re: [gmx-users] output logfile

Hi Sanku The ^M ‘s in that sample indicate a line break that was issued by a different text formatting standard. This frequently happens if files are generated in one OS say Windows then viewed in another say unix. Is your version of gromacs compiled for your system or was is compiled for a dif

[gmx-users] Re: grompp error for CNT simulation

>  Dear gmx users, > I am using gromacs 4.5.3 to simulate CNT in water. up to now I have done > these things: > 1. I used packmol to create my PDB file and the used editconf to change PDB > to gro file. > 2. I copied oplsaa.ff folder in my working directory > 3. I added following lines to atomname2

[gmx-users] Convert xpm to matrix

Dear all,   I'd like to convert an xpm file to delimited CSV , because I need to import values in excel.   Any suggestion?   Thanks-- 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/Ma