[gmx-users] g_hbond for trajectory without having box information

[bipin singh]

According to the suggestion I added the box to the trajectory using -box
option of trjconv, using the following commands:

trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc

then using the g_hbond on the output trjectory (traj_box.xtc) run
successfully but gives the wrong number of H-bonds between the proteins
atoms.

I have also tried to process the output trajectory (traj_box.xtc) with
trjconv using -pbc mol -ur compact options before using g_hbond, but again
I have got wrong number of H-bonds.

Please help me to rectify the error.


On Fri, Jul 19, 2013 at 11:19 AM, bipin singh <bipinelmat at gmail.com> wrote:

> Thanks a lot Prof. David. I will try this.
>
>
> On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel <
> spoel at xray.bmc.uu.se> wrote:
>
>> On 2013-07-19 06:26, bipin singh wrote:
>>
>>> Hello all,
>>>
>>> I was using g_hbond to calculate H-bonds for a trajectory made from
>>> several
>>> individual snapshots from MD simulation, but because this trajectory does
>>> not have the coordinates/information for simulation box, g_hbond is
>>> giving
>>> the following error:
>>>
>>> Fatal error:
>>> Your computational box has shrunk too much.
>>> g_hbond_mpi can not handle this situation, sorry.
>>>
>>>
>>> Please let me know, if there is any way to rectify this error.
>>>
>>>
>>>  you can add a box to your trajectory using trjconv.
>>
>> --
>> 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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>
>
>
> --
> *-----------------------
> Thanks and Regards,
> Bipin Singh*
>



-- 
*-----------------------
Thanks and Regards,
Bipin Singh*