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

2014-11-06 Thread Chris Papamitrou 
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 ?




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conceptions.  Infinitely varied in its effects, nature is simple only in
its causes, and its economy consists in producing a great number of
phenomena, often very complicated, by means of a small number of general
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Re: [gmx-users] Umbrella sampling ignore hydrogen command -ignh

2014-11-06 Thread 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

--
==

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

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

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