[gmx-users] Ion Parametrization in OPLS-AA forcefield
Dear All, I require the papers in which the original parameters (in ions.itp) for ions in OPLSAA force field was published. Also I would like to if there are any studies in which these ion parameters were benchmarked with experimental values. Thanks a lot. Regards Srinivas -- Srinivas Ramachandran Graduate Student Molecular and Cellular Biophysics Program Department of Biochemistry and Biophysics University of North Carolina at Chapel Hill USA www.unc.edu/~ramachan ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
[gmx-users] xpm format
Hi All, I would like to use g_mdmat to construct a distance matrix. But the only option for output is xpm format. How should I proceed if I want to get a numerical matrix? Is there any script to decode xpm to a numerical distance matrix? Regards Srinivas Ramachandran ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
[gmx-users] Relative Constraints on atoms
Dear all, I know that we can place harmonic constraints on selective atoms, specified by an index file. But this only ensures that the atom position remains same throughout the simulation. But if I only want two atoms' positions to remain same only relative to one another but the atoms can move otherwise, is there any way to do this? I want to know this because I want a fragment of the protein to remain alpha helical throughout the simulation, but I dont want it to conserve its original co-ordinates. Regards Srinivas Ramachandran ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
