[gmx-users] intermolecular H bond selection

[Erik Marklund]

21 maj 2012 kl. 06.54 skrev 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

And if you have many alanines you might have to call g_hbond many times (think in the lines of scripting). Or invoke g_hbond once with the index group consisting of all alanines chosen twice and decompose the hbonding matrix (-hbm -hbn) yourself (python/perl).

Best,

Erik

>  
> 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
> 
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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