[gmx-users] residue-residue interaction energies

[Justin Lemkul]

On 10/8/12 3:14 AM, federico vaglio wrote:
> Hi Justin,
> thank you for your quick reply.
>
> When you say:
>
> "..Probably by analyzing them individually with mdrun -rerun to recalculate
> each frame.  Tedious, but can be easily scripted..."
>
> do you mean I have to run g_enemat module using -b and -e options in order
> to set the first and the last frame to read from trajectory?
> If not, could you please suggest me the correct way to do so?
>

Not what I was suggesting, but using -b and -e should also work.

-Justin

> thank you again.
>
> Federico
>
> On Sat, Oct 6, 2012 at 4:54 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/5/12 1:40 PM, federico vaglio wrote:
>>
>>> Dear all,
>>> I would like to extract the interaction energies (LJ
>>> and electrostatic) between each residue pairs from my trajectory.
>>> The g_enemat tool generates only 3 xpm image files (Coul-SRemat.xpm,
>>> LJ-SRemat.xpm, totalemat.xpm) but not a "data" file with
>>> the residue-residue interaction energies I'm looking for.
>>> Is there a way to get these numbers? Or have I to read the xpm "matrix"
>>> and
>>> convert all those letters to the corresponding energy values?
>>>
>>
>> Yes, you have to map it out based on the .xpm labels.
>>
>>
>>   Finally, is there a way to get pairwise residue-residue interaction energy
>>> values from each snapshot of my trajectory ?
>>>
>>>
>> Probably by analyzing them individually with mdrun -rerun to recalculate
>> each frame.  Tedious, but can be easily scripted.
>>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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