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

[bipin singh]

Sorry for my silly mistake.

I have a doubt regarding the expected difference in total No. of H-bonds
calculated with whole a MD trajectory (protein+solvent box) and H-bonds
calculated with concatenated frames (only protein) from a MD trajectory.

 I mean, will the number of H-bonds present at a particular time in a MD
trajectory (protein+solvent), should be exactly same as number of H-bonds
calculated using trajectory made of concatenated frames (only protein) from
(if we look at number of H-bonds present at same point of time in both).

Because I am not getting the exact match between the two, there is random
difference of 1-3 H-bonds at some point of time.


On Fri, Jul 19, 2013 at 2:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/19/13 4:17 AM, bipin singh wrote:
>
>> 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.
>>
>>
> A 0.9-nm cubic box is likely too small to correctly accommodate even an
> amino acid, let alone an entire protein.
>
> -Justin
>
>
>> 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*
>>>
>>>
>>
>>
>>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
>
> ==============================**====================
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-- 
*-----------------------
Thanks and Regards,
Bipin Singh*