Thanks for the suggestion Xavier. However, I already tried g_mindist and the problem is that it does not use the center of mass of the reference group to calculate the distance to the atoms of the solvent group. Instead, it computes all possible distances between pairs of atoms between the groups at a given time and gives the minimum distance from any of the atoms in the reference group it finds.
Perhaps if there is a way to input coordinates to represent a dummy atom then use g_mindist to calculate the distance and number of contacts between the dummy atom and each solvent atom within the cutoff range that would give me the estimate that I am looking for. Thanks, Yolanda On Fri, 05 May 2006 08:53:07 +0200, "X.Periole" wrote: > On Thu, 4 May 2006 23:48:28 -0400 (EDT) > "YOLANDA SMALL" <[EMAIL PROTECTED]> wrote: > > Hello, > > > > I would like to determine the percentage of water > >occupation in a protein region > > by calculating the distance between the center of mass > >of a group of atoms and > > the solvent. Does anyone know which gromacs tools can > >provide an estimate of > > this information? By the way my trajectory is in xtc > >format. > > > > you could try g_mindist, which gives the minimum distance > between 2 groups and counts the number of contacts (water) > within a given distance from a group (protein). > > you could also see if trjorder coudl help. It orders a > group > (solvent) by distance to a give grou (protein). > > XAvier _______________________________________________ gmx-users mailing list gmx-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
