[gmx-users] adding mixed solvent using genbox

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jul 24 08:04:20 CEST 2007

shankari hariharan wrote:
> Dear Users,
> I want to simulate a box which consists of glycine(32), water(1000) and 
> ethanol (130).
> 1. I used geconf to generate the glycine.gro file with the required 
> number and at a particular distance.
> 2. Then I used genbox to solvate the molecules.
> I couldn't understand the option of adding mixed solvent in genbox. 
> Kindly give me suggestion to add ehanol to the system

Please spell things correctly... computers, science in general, and 
computational chemistry in particular, require you to be exact when 
describing things. Failing to do so makes people wonder what else you're 
doing wrongly... and whether you're worth their time answering.

There's no ready way to solve the above problem with standard GROMACS 
tools, as you'd know from reading the genbox documentation. Easiest is 
to use some molecule editor to get your glycine and ethanol numbers 
right, and then to solvate that to get 1000 waters. Or you could make 
building blocks of ethanol and ethanol+glycine in the same size block 
and play Lego with genconf to get 32+130. Then equilibrate for a while 
to break the system symmetry.


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