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
--
==================================================
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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