[gmx-users] genbox nmol add water

Dallas Warren dallas.warren at vcp.monash.edu.au
Mon Mar 21 22:34:03 CET 2005

>how can I manage to put a certain number of water molecules in a box? I 
>tried the genbox -nmol option with -ci spc216.gro, but it didn't work out 
>due to "more than one residue". Can I convert the spc216.gro file so that 
>it'll contain only one residue (and how) or is there a better way? I need 
>to have the same number of molecules in a box, if I want to do free energy 
>calculations, right?

copy the spc216.gro to something like spc.gro or h2o.gro, then text edit 
the file, deleting all put the first three atoms, adjust the second line to 
the correct number of atoms, and reduce the box size.  You can then use 
genbox, but the code behind it isn't that good as you may end up with some 
high energy overlaps. But with something as simple as water a quick energy 
minimisation should sort that out.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9574
When the only tool you own is a hammer, every problem begins to resemble a nail.
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