[gmx-users] g_mdmat question

SUSAN VARNUM huskyrunnr at msn.com
Fri Mar 16 00:49:00 CET 2007

Dear gmx users,

I have a question about g_mdmat, related to a question I posed earlier.  I know a bit more now.  When I run the command on a trajectory in pdb format, either using -b and -e to specify which string of frames to average over, or just leaving -b, -e unspecified, I get a contact map that is  not an average but is identical to the contact map of the structure in the last frame that is read.  It does not matter whether I specify -mean or leave it out and run default.  I have verified that averaging is not happening by using the -frames option and comparing the maps of the individual structures to my attempted average maps.  I need some help/suggestions of what I might be doing wrong.

Thanks for any help you can give,

David Lowry 
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