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

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 A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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