[gmx-users] Constraining hydrogen - heavy atom bonds with different naming.
addiw7 at googlemail.com
Tue Mar 1 19:42:39 CET 2016
Oh gosh..., so in that case is there any other way around to constraint
those MH11 - MCB1 etc. bond lengths except for renaming all hydrogen atoms?
2016-03-01 19:29 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> On 3/1/16 1:24 PM, Dawid das wrote:
>> Dear Gromacs Experts,
>> I am pretty sure I have already answered this question long time ago but I
>> cannot find
>> it. What I did is I added a new residue for my system and it contains
>> hydrogen atoms.
>> Now, the thing is that all atoms names start with "M", so I have MH21,
>> MH22, MCA1, etc.
>> atoms. I want to constrain hydrogen - heavy atom bonds:
>> constraints = h-bonds
>> and I am not sure whether I constraint those novel hydrogens. In other
>> words, how does
>> Gromacs 5.0.4 know that my atom is a hydrogen? Based on atomic number in
>> ffnonbonded.itp or based on atom name/type?
> It's based on name. If the first character is H, it is added to the
> constraint list. So your case will not work. You can always confirm what
> is constrained by using gmx dump on the .tpr file and looking for F_CONSTR.
> 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
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