[gmx-users] radius of gyration taking bound water into account

Dear users, in computing radius of gyration of a protein in water (g_gyrate), I have found values that are rather smaller than what found experimentally, maybe because bound water isn't taken into account within g_gyrate routine. Is there any way to overcome this limitation? Thanks in

[gmx-users] question about g_rmsdist II

Sorry, since I hadn't any answer to my question yet, I'm resending it to give it visibility! Thanks, Fabrizio --- Messaggio inoltrato --- Da: Fabrizio Mancinelli [EMAIL PROTECTED] A: gmx-users@gromacs.org Oggetto: question about g_rmsdist Data: Mon, 14 May 2007 18:52:54 +0200 Dear all

[gmx-users] question about g_rmsdist

Dear all, I would like to have some elucidation about g_rmsdist output. Optionally, it outputs three matrices with the options -rms, -mean and - scl. Questions are: 1) Exploring .xpm files, I see there is a letter code which converts color exa-codes to letters to values. The resolution is

[gmx-users] do_dssp, -map option

Dear users, I would like to have some delucidations about the -map option of the do_dssp routine. In the help file, it says File that maps matrix data to colors, and I guess it is an input file to be supplied in order to assign colors to the different ss elements. Is it right? And, if so, how

[gmx-users] Segmentation fault in disco

Hi all, I tried to perform a CONCOORD simulation by means of cdist and disco routines included in GROMACS. However, while cdist appears to work well, disco produces a segmentation fault error. Maybe a problem in managing memory? Does anybody give me a clue? Thanks in advance! -- Fabrizio