[gmx-users] SImulation with urea

bharat gupta bharat.85.monu at gmail.com
Wed Mar 5 00:10:34 CET 2014


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


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