[gmx-users] g_dist and vsites

Joe Joe ilchorny at gmail.com
Tue Mar 9 19:16:50 CET 2010


On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> On 2010-03-09 19.09, Joe Joe wrote:
>> Hi I am trying to post process and xtc trajectory using g_dist. I am
>> trying to calculate the CA-CB distance of an Alanine residue but I get
>> NAN in all the distance columns. It works for the other residues I've
>> tried (i.e. SER, VAL). I am using vsites in my simulation and I think it
>> may have some thing to do with the way gromacs outputs the CB positions
>> in the xtc file when the CB is part of the vsite network. Any thoughs?
>> Thanks,
>> Ilya
>>  Are you sure your index file matches the xtc/tpr?
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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