[gmx-users] g_dist and vsites

[Joe Joe]

I  trjconv/ed xtc to pdb and loaded into vmd. The coordinates looked fine.

I also

tpbconv/ed topol.tpr to topol_subset.tpr.

then I

editconf/ed topol_subset.tpr to gro and looked at the coordinates. Index
file matched and structure looked whole in vmd.

I will try the gmxdump

Thanks,

Ilya




On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> On 2010-03-09 19.16, Joe Joe wrote:
>
>> yep.
>>
> Have you gmxdump/ed the xtc to check the coordinates are right?
>
>>
>> On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
>> <spoel at xray.bmc.uu.se <mailto: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 <mailto:spoel at xray.bmc.uu.se>
>>
>>    http://folding.bmc.uu.se
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>
> --
> 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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