[gmx-users] specialized solvents

[Erik Lindahl]

Hi David,

I've done some alcohol simulations (about 13% Ethanol and tannine,  
approximating a California Cabarnet :-).

The equilibration is pretty fast for these types of systems, so instead  
of trying to figure out a smart way of getting a good distribution I  
just randomly placed a number of EtOH molecules in a box, added water,  
and then ran it unattended for 2 days until the density had  
equilibrated.

The command genbox has some options you can use to place molecules in  
boxes, and the easiest way to control the number of water you add later  
is to change the box dimensions with editconf and then just rerun the  
genbox program to add water (takes a couple of seconds).

You can also edit the coordinate file and topology to have the right  
number of CH4 / water molecules - atom/molecule numbers don't have to  
be continuous, we just check that the number is different from the  
preceding atom/molecule.

If you want to add impurities to water when simulating e.g. a protein,  
you can use the program genion to create ions or united-atom CH4 (a  
single site). I'm pretty sure it would also work to manually replace a  
water molecule with an all-atom CH4 in the coords+topology and then run  
energy minimization. If it doesn't, look at the options to do soft-core  
interaction runs!

Cheers,

Erik



On Tuesday, Mar 18, 2003, at 17:57 US/Pacific, David Kendall wrote:

> I am trying to create a solvent that has a lot of water and a little  
> bit of impurity. Something like 100 molecules of H2O and 1 CH4, but I  
> am spinning my wheels trying to figure out how to do it. Has anyone  
> out there created their own solvents and could give me a HOW-TO on it?
>
>  
>
> David
>
>
------------------------------------------------------------------------ 
-----
Erik Lindahl, MSc, PhD     <lindahl at stanford.edu>
D109, Fairchild Building
Dept. Structural Biology, Stanford University School of Medicine
Tel. 650-7250754    Fax. 650-7238464

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