[gmx-users] (no subject)

Hi all, i 'm a beginner in molecular dynamics. I was doing the tutorial of md group, hydration free energy of toluene : http://md.chem.rug.nl/education/Free-Energy_Course/2.hydration-fe.html i have some problems regarding the calculation of toluene in water. the thing is that in the examples file

Re: [gmx-users] toluene tutorial sc-power value

Hi MaiK, Sorry i forgot the subject. Thank you to have answered this email. This tutorial is about solvation free energy of toluene using thermodynamical cycles. two energies have to be calculated according to this cycle, the hydration energy of toluene and the mutation energy from dummy to toluene

Re: [gmx-users] toluene tutorial sc-power value

Hi maik the energy DEltaG_hyd=deltaG_mutation(vacuo)-deltaGmutation(water) for fisrt one deltaG_mutation(vacuo) =-2,85 for second deltaGmutation(water) =15,87 so i found DEltaG_hyd = -19 kj/mol instead of -3,1 kj/mol i'll do a series of calculation with sc-power=2 and see the difference see if

Re: [gmx-users] toluene tutorial sc-power value

hi concerning the cycle i saw this error since i started the tutorial, i paid attention to that but as you said it's not that important since my energy value is too high. i'm right now doing the problem again with sc-power=2 and also 10 points is it enough to have an approximate correct value sinc

Re: [gmx-users] toluene tutorial sc-power value

Hi maik I made the calculation with sc-power=2 adding 3 lambda values. Now i get integrating the plot of average free energy for the mutation of toluene in water 0.559 instead of 15,8 in previous calculation. if i combine with the free energy in vacuo i have -3,41 KJ/mol vs (-3,1 KJ/mol exp.). This

Re: [gmx-users]build topology file for a molecule define with new residues

in telling me the main steps to create those files? geraldine cilpa Helsinki university ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

Re: [gmx-users]build topology file for a molecule define with new residues

gt;> >> http://wiki.gromacs.org/index.php/Exotic_Species >> >> >> The PRODRG server can be used to generate primitive GROMOS topologies, >> but be advised that the charges given in these topologies are often >> unsatisfactory. >> >> -Justin >> >>

[Fwd: Re: [gmx-users]build topology file for a molecule define with new residues]

Hi all, Is anybody has already done umbrella sampling for a free energy calculation? There are some theoretical documentation but not so much information on how to do that in practice. For me it's the first time. could anybody know how for pulling or approaching two biomolecules and step simulation

Re: [Fwd: Re: [gmx-users]build topology file for a molecule define with new residues]

thank you, check the site given in the post but there's no tutorial but i least the dissertation of the guy doing those calculations, i could check that. thanks for suggesting me geraldine On Tue, August 19, 2008 1:15 pm, Justin A. Lemkul wrote: > > > [EMAIL PROTECTED] wrote: >> Hi all, >> Is a