[gmx-users] intermolecular H bond selection

[Anirban]

On Mon, May 21, 2012 at 3:09 AM, mu xiaojia <muxiaojia2010 at gmail.com> wrote:

> Thanks for prompt answering but I may need to clarify my question and
> sorry for the understanding,
>
> For example, I have dipeptides like Ala-Ala, how to ask g_hbond only
> calculate the h bonds between Ala on different dipeptides instead of
> counting all the possible h bonds between Ala(intermolecularly and
> intramolecularly)
>
>
Make two groups with make_ndx that contains the residue numbers (or
specific atom numbers) of the ALA residues between which you want to count
the H bonds and then select these group numbers with g_hbond.

-Anirban


> Thanks very  much!
>
>
> On Fri, May 18, 2012 at 7:57 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 5/18/12 7:22 PM, mu xiaojia wrote:
>>
>>> Hi gmx-users,
>>>
>>> I have a question might be explained before but I cannot understand from
>>> the
>>> previous , how to calculation the intermolecular h-bonds between two
>>> molecules?
>>> I saw someone mentioned using a second tpr file, but how to do it
>>> specifically?
>>> Thanks very much!
>>>
>>>
>> g_hbond asks for two index groups to be selected.  Assign each molecule
>> to an index group and select them when prompted.
>>
>> -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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