[gmx-users] hydrogen bond calculation problem

[Justin Lemkul]

On 11/11/13 12:36 PM, Sushma Yadav wrote:
> Dear gromacs users,
>
> I have NaCl-water system of finite concentration .I want to calculate
> water-water hydrogen bond in the first solvation shell around ion..So I
> used g_hbond -shell option.For single ion in water,its easy to
> calculate..But say,for water-water hydrogen bonds around two Na+ ions,it is
> saying to Select one atom for shell. Although I have more than 1 Na+ ions
> and I want to see water-water hydrogen bond around all Na+ ions
> simultaneously.Is it possible to take solvation shell of each ion at a same
> time?
>

According to the help description for the -shell option, no.  Only one particle 
can be considered at a time.  You'll have to analyze each Na+ separately, which 
is easily scripted.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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