[gmx-users] Re: How to set the density of the box?

Vitaly V. Chaban vvchaban at gmail.com
Thu Apr 15 08:41:41 CEST 2010

>>       Hello, I want to set the density of the box (e.g. set 1 g/ml for
>> the water box). I use the density option in the editconf, then use the
>> genbox to generate the box, but the result of the density is not what I
>> setted. How can  I do ?

It seems to be much easier in your case to calculate the needed MD box
dimensions by hand and edit your conf.gro (last line). You have mass
of the box and you have the desired density, so the volume =

>>       I have another question, I don't find the tip3p.gro and spce.gro
>> water model  in the top file, only have the .itp document. if I want to
>> generate the TIP3P water box, how can I do, or  where can I get the
>> tip3p.gro and spce.gro documents?

You may use spc216.gro as a starting point for all 3-opint waters. As
MD runs, SPC "will become" TIP3P or other one based on the data in ITP
topology file.

Dr. Vitaly Chaban

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