[gmx-users] Hydrogen bond with chlorine

Justin Lemkul jalemkul at vt.edu
Mon Feb 10 16:04:51 CET 2014

On 2/10/14, 9:52 AM, Jianguo Li wrote:
> Hi Dhawal,
> One way you can try is to manually change the name of chloride to oxygen so that the g_hbond code can treat the new atom name as acceptors. Just modify .gro file, .top file and ions.itp file and get a new tpr file. And use the rerun option of mdrun to get a new trajectory.  Then you can calculate the hbond using the new trajectory.

We've used this trick before.  You don't actually even need to rerun the 
trajectory.  Given that .xtc and .trr files don't store atom names, the 
coordinates that were originally Cl are simply mapped to O in this case.



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

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


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