[gmx-users] intermolecular H bond selection
reach.anirban.ghosh at gmail.com
Mon May 21 06:54:10 CEST 2012
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
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.
> 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
>>> previous , how to calculation the intermolecular h-bonds between two
>>> I saw someone mentioned using a second tpr file, but how to do it
>>> 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 A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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