[gmx-users] How to add small molecule in the solvent?
feenstra at chem.vu.nl
Tue Jan 20 10:01:12 CET 2004
> On Wed, 2004-01-14 at 21:24, Yuhua Song wrote:
>>The situation is that I have a equilibrated systems of biomembrane in a box
>>of water and the ions in the solvent. Now, I want to add some small
>>molecules into this equilibrated system of solvent. In this situation, what
>>should I do?
> you can add indidividual molecules with genbox
> alternatively you can grow a molecule using FEP. See recent mailing list
> posts for this.
Or, you may try adding your additional molecules 'on top' of the water,
then sort your water with respect to distance to these new molecules
(you can do that with trjorder, it can also accept a single .pdb or .gro
file in stead of a trajectory file and a .tpr file). Then, you can
find how many of the first water molecules (trjorder will have put the
closest waters first) are too close, and remove them. It's a bit of work,
but it can be done!
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
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