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

[Justin Lemkul]

On 7/19/13 6:55 AM, bipin singh wrote:
> 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.
>

I suspect that the issue stems from having to manually set the box.  I don't 
understand why you would have to do this after running a simulation in explicit 
solvent.  Did you just extract the protein coordinates from the explicit 
simulation?  If so, I don't see how the box information would be omitted.

You can get spurious H-bonds across PBC if you are manually setting a bad box 
size in a given frame or series of frames.  Without the exact sequence of 
commands from what you have done, it's pure guesswork.

-Justin

>
> 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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>
>
>

-- 
==================================================

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 | (410) 706-7441

==================================================