[gmx-users] adding mixed solvent using genbox

Yang Ye leafyoung at yahoo.com
Tue Jul 24 16:03:42 CEST 2007

On 7/24/2007 1:54 PM, 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
If you can throw away the possible bias of initial configuration to the 
simulation results, what you can do is to in step 2 is

2.1. Solvate the system with >1000 (e.g.: 1300?) water first.
2.2 Remove some water, say 100
2.3 add ethanol using genbox
2.4 if there is not enough ethanol, go to 2.2.

Then really equilibrate your system well by running long time simulation 
and high temperature. Glycine can be fixed with position restraints.

The problem here is no randomness is random.
> Thanks in advance
> regards,
> shankari
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