[gmx-users] Umbrella sampling ignore hydrogen command -ignh

[Justin Lemkul]

On 11/6/14 4:53 PM, Chris Papamitrou wrote:
> I am trying to perform a simulation regarding the effect that hydration has
> on tensile response for my system.  When i looked into the umbrella
> sampling tutorial it said to create a start file using the
>
> pdb2gmx -f input.pdb -ignh -ter -o complex.gro
>
> command and was wondering what effect that the -ignh option had on my
> simulated results?  do the hydrogens
> not get accounted for in this simulation, and if so, how are the
> atomic bonds in which the hydrogens are
> supposed to be located treated in terms of replacing those hydrogens?
> does this mean i am doing a
> united atom model ?
>

Start with pdb2gmx -h.  The -ignh has a very simple purpose, and it's used 
mostly for working around nomenclature issues.

Whether or not you use a united-atom force field is entirely up to you, based on 
what you choose.

-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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