[gmx-users] using g_hbond between index gps of specific

[Justin Lemkul]

On 12/5/14 7:31 AM, soumadwip ghosh wrote:
> Dear Erik,
>               Thats how I have calculated the h-bond number and
> distributions between chain_A and chain_B .Is there a way to freeze Na in
> chain A(say) and then calculate the h-bonding with chain_B? I hope you get
> that I want to calculate the h-bonding between chain_A and chain_B in
> presence of sodium as well. Now how to do that? Will it be useful if I
> calculate h -bonding at different time gaps using -b and -e flags assuming
> that the system will be more perturbed by sodium towards the end the
> simulation?Is it required to incorporate Na ions in any of the chain by
> group merging? Or there is an alternate way out?
>

As has been said a few times, the Na ions do not factor into the groups used for 
H-bonding analysis at all.  You need two groups - chains A and B - neither of 
which need to include Na, because Na is not going to be recognized by g_hbond as 
participating in any sort of hydrogen bonding.  The Na has exerted its effects 
during dynamics, not during analysis.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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