[gmx-users] adding mixed solvent using genbox

David van der Spoel spoel at xray.bmc.uu.se
Tue Jul 24 13:20:39 CEST 2007

Mark Abraham wrote:
> 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.

You can start by making an equilibrated alcohol solution with slightly 
more than 32 ethanol/130 waters (this is important).

Then you pass the the relaxed eth/wat mix to genbox as a solvent. excess 
solvent you remove using emacs or similar text editor.

> Mark
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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