[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.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
More information about the gromacs.org_gmx-users