[gmx-users] Mix two solvents
André Farias de Moura
moura at ufscar.br
Tue Aug 10 20:34:57 CEST 2010
you can manually edit one of the gro file to increase the length in one
direction by an arbitrary amount, then use genbox:
genbox -cp <edited file> -cs <the other gro file>
(I just did that with water and methanol from the gromacs tutorials,
works just fine)
maybe set -vdwd to an adequate value to prevent insertion of molecules
of second type on the wrong side of the box...
> Use the same box size for both. Then move one box with eidtconf
> -translate by its boxlength. Afterwards, you can simply put the boxes
> together to one large one.
> Quoting teklebrh at ualberta.ca:
>> Dear Gromacs,
>> I want to combine two separately equilibrated solvents into one mixed
>> solvent file. How can I do that? I want to check the mixing effect of
>> those solvents and try to check the density and volume change before
>> and after mixing those solvents. I have equilibrated and run MD for 2ns
>> for each solvent and the density I got is pretty the same as of the
>> experimental value. But now I want to combine both these files into one
>> .gro file so that to see the volume/density change after MD and
>> calculate the mixing effect. Can anybody help me on this issue?
>> Thank you
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