[gmx-users] SImulation with urea

Justin Lemkul jalemkul at vt.edu
Wed Mar 5 00:16:26 CET 2014

On 3/4/14, 6:10 PM, bharat gupta wrote:
> Hi,
> I have some small doubt regarding using urea in simulation. Actually, I
> calculated the the number of urea molecules for a particular concentration
> in the box. For eg., the same box if filled with water occupies 43614
> molecules of water and if I need to fill molecules of urea for 1M
> concentration, the values comes around 875. I added, those urea molecules
> using -ci and -nmol flags in genbox command. How to add the water now, i.e.
> the remaining 42379 water molecules. When I use genbox to add water it
> replaces those Urea molecules completely and add 43614 molecules. I even
> tried adding water and urea simultaneously, in that case the urea molecules
> are added as per the given number, but the number of water molecules added
> are lesser than 42379, which should be 43614. What am I going wrong ??
> For adding water and urea simultaneously, I used the following command:
> genbox -cp newbox,gro -cs spc216.gro -ci Urea.gro -nmol 875 -o solv.gro -p
> topol.top

Doing these two processes simultaneously is asking for trouble and will probably 
fail.  I don't understand the statement above about genbox removing urea - the 
program shouldn't do that (genion replaces molecules, genbox adds them).  Do the 
additions in two steps:

1. Add urea with -ci -nmol
2. Simply fill the rest of the box like would would anything else with genbox 
-cs spc216.gro -cp system_with_urea_already_added.gro



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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