[gmx-users] intermolecular H bond selection

[mu xiaojia]

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)

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
>
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