<br>Hi Sven,<br><br>1. Before using genconf, make the box for one glycine larger. If you have a distance of 0.5 nm to the wall originally, you will allow about four layers of water between any two adjacent glycines.<br>2. As has been stated before, simulating for a short while will allow the solution to randomize.
<br>3. Making your box larger has nothing to do with your cutoff. <br><br>Cheers,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 11/2/05, <b class="gmail_sendername">Sven Huttenhouse</b> <<a href="mailto:mdsimulation@hotmail.com">
mdsimulation@hotmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>Thank you all for your reply<br>actually I genarated 200 glycine molecules by replicating one molecule using
<br>genbox abd it gave me molecules that are randomly disrtibuted but attached<br>to each other. I then used genconf to generate the the molecules and it gave<br>me 200 molecules that are not attached but also not randomly distributed.
<br>When I use editconf to generate a box aroud the molecules (generated by<br>genconf) and then genbox to solvate them in water I notice that water<br>molecules are located around the 200 molecules and no water molecules comes
<br>withen the 200 glycine molecules.<br>what I'm looking for is to get 200 glycine molecules not attached to each<br>other and randomly distribulet in a box of water molecules. How can I get<br>this?<br><br>One more thing, when I change the bex dimentions using option -d in editconf
<br>this will affect the cutoff distance is this ok?<br><br>kind regards<br>Sven<br><br>>From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>>Reply-To: Discussion list for GROMACS users <
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>Subject: Re: [gmx-users] question about genbox
<br>>Date: Wed, 2 Nov 2005 06:24:51 +0100<br>><br>>Hi Sven,<br>><br>>Just to add a word on Dallas' reply. Use a larger box, such that you get<br>>just over the number of water molecules you need. Then delete the surplus.
<br>>Pressure coupling will fix the vacuum.<br>><br>>Cheers,<br>><br>>Tsjerk<br>><br>>On 11/2/05, Dallas B. Warren <<a href="mailto:Dallas.Warren@vcp.monash.edu.au">Dallas.Warren@vcp.monash.edu.au</a>
> wrote:<br>> ><br>> > Sven,<br>> ><br>> > > I'm trying to solvate 200 molecules of Glycine in water and I need a<br>> > > certaine concentration in the box. How can I determine the<br>
> > > number of water<br>> > > molecules to be added to the glycine. when I run the genbox<br>> > > command it gives<br>> > > me 1712 water molecule and I need them to be 2650 instead.<br>
> ><br>> > Couple of options, save a smaller number of waters in a gro file and<br>> > tell genbox to add the correct number of those (not sure if it has<br>> > improved, but this script use to get some molecules overlapping and with
<br>> > bad contacts, so take care). Or adjust the dimensions of the box using<br>> > editconf until you get the correct number of water molecules added when<br>> > you solvate it.<br>> ><br>> > Catch ya,
<br>> ><br>> > Dr. Dallas Warren<br>> > Lecturer<br>> > Department of Pharmaceutical Biology and Pharmacology<br>> > Victorian College of Pharmacy, Monash University<br>> > 381 Royal Parade, Parkville VIC 3010
<br>> > <a href="mailto:dallas.warren@vcp.monash.edu.au">dallas.warren@vcp.monash.edu.au</a><br>> > +61 3 9903 9073<br>> > ---------------------------------<br>> > When the only tool you own is a hammer, every problem begins to resemble
<br>> > a nail.<br>> > _______________________________________________<br>> > gmx-users mailing list<br>> > <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a>.<br>> ><br>><br>><br>><br>>--<br>><br>>Tsjerk A. Wassenaar, M.Sc.<br>>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>>Dept. of Biophysical Chemistry<br>>University of Groningen
<br>>Nijenborgh 4<br>>9747AG Groningen, The Netherlands<br>>+31 50 363 4336<br><br><br>>_______________________________________________<br>>gmx-users mailing list<br>><a href="mailto:gmx-users@gromacs.org">
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<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>