karim trust is good.
one possible method to generate your initial configuration is to do monte carlo insertions of solvent molecules until the desired numbers of each are present in your box. this method has the advantage that the box will be truly mixed. there are probably many codes out there to do this, but i use music by the snurr research group (http://zeolites.cqe.northwestern.edu), which allows you to stop a grand canonical monte carlo sim (constant mu,v,t) when user-defined criteria have been met. if you choose to use this method, be warned that you'll have to do a really thorough energy minimization before launching your md. cheers mo --- [EMAIL PROTECTED] wrote: > Message: 5 > Date: Thu, 27 Apr 2006 11:03:03 +0430 > From: "Mahnam" <[EMAIL PROTECTED]> > Subject: [gmx-users] Mix solvent > To: [email protected] > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain > > > In God We Trust > Hello GMX users > I want to use gromacs program to study a protein in > a solvent of the mixture > of 30% methanol and 70% water. Would you please > tell me how can I make gro > file of "mix solvent" box for genbox. > Thank you very much in advance > Karim Mahnam > Institute of Biochemistry and Biophysics (IBB) > Tehran University > P.O.box 13145-1384 > Tehran > Iran > http://www.ibb.ut.ac.ir/ > > > > > ------------------------------ > > Message: 6 > Date: Thu, 27 Apr 2006 18:30:38 +1000 (EST) > From: "Mark Abraham" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Mix solvent > To: "Discussion list for GROMACS users" > <[email protected]> > Message-ID: > > <[EMAIL PROTECTED]> > Content-Type: text/plain;charset=iso-8859-1 > > > > > In God We Trust > > Hello GMX users > > I want to use gromacs program to study a protein > in a solvent of the > > mixture > > of 30% methanol and 70% water. Would you please > tell me how can I make > > gro > > file of "mix solvent" box for genbox. > > There's no straightforward approach that I'm aware > of. One possibility is > to do the arithmetic for the size box you want to > use and generate a > smaller box filled with N water molecules that will > give you 70% were you > to increase the size of the box and fill the gaps > with methanol. Then > increase the size of the box, and use the -nmol and > -ci options to genbox > to add enough methanols to make the mix 70/30. Then > you will need to > equilibrate that box for a while to get a good mix > of solvents at > reasonable density and pressure. I think you should > be able to use that > box later for subsequently doing genbox for your > protein. > > You could also manually delete enough waters to get > down to 70%, and use > the genbox options above to try to fill the gaps, > but you will have a hard > time fitting methanol into water-sized holes. > > Mark > > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > > > End of gmx-users Digest, Vol 24, Issue 90 > ***************************************** > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
