[gmx-users] Distance computation using g_mindist
spoel at xray.bmc.uu.se
Tue Jul 6 16:54:39 CEST 2004
On Tue, 2004-07-06 at 16:45, sunita at chem.iitb.ac.in wrote:
> Dear gmx-users,
> In the manual it is mentioned that g_mindist computes the distance between
> one group and a number of other groups. Does it calculates the minimum
> distance between the center of mass of of one group with that of other for
> a given time or it computes all possible distances between a pairs of
> atoms in the specified groups at a given time and give the minimum
> distance out of it.
> Another question is that I have calculated the distance between amide
> proton as one group and SOL as another group. The .xvg file shows the time
> vs distance graph. The atm-pair.out file gives the atom id of
> corresponding groups at a given time. From there I found that distance is
> not between the NH proton but from N atom to HW1 of SOL though I had
> specified explicitly one group as amide proton. Randomly I checked the
> id's of SOL and it is always the HW1 but not HW2 or OW.Could I know how
> does g_mindist program selects the index groups.
And is it wrong?
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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