[gmx-users] Thermodynamic Integration Glu -> Ala Mutation

Dear Gromacs Users, I am trying to find out the relative free energy difference of binding of a ligand with wild type protein (Glutamate residue) and mutant protein (Alanine residue). For charge part of the mutation, this is what I'm planning to do: ; residue 40 GLU rtp GLU q -1.0 552 opls

Re: [gmx-users] thermodynamic integration with implicit solvent

Samrat Pal wrote: Hi All, Is it possible to use thermodynamic integration method with implicit solvent model in gromacs 4.5.4? Try it and see, but you may have stability issues in some algorithms with one of your end states, wherein the system is essentially nothing. How does on

[gmx-users] thermodynamic integration with implicit solvent

Hi All,    Is it possible to use thermodynamic integration method with implicit solvent model in gromacs 4.5.4? Thanks Samrat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/

Re: [gmx-users] thermodynamic integration yields different values in gromacs 3.3.1 and later versions

schn...@uni-heidelberg.de wrote: Dear Gromacs users, I am doing thermodynamic integration in order to compute the change in free energy upon increasing the electric charges of a water molecule from zero (lambda=0) to its actual partial charges (lambda=1). I get significantly different results

[gmx-users] thermodynamic integration yields different values in gromacs 3.3.1 and later versions

Dear Gromacs users, I am doing thermodynamic integration in order to compute the change in free energy upon increasing the electric charges of a water molecule from zero (lambda=0) to its actual partial charges (lambda=1). I get significantly different results of with Gromacs 3.3.1 on one hand a

[gmx-users] Thermodynamic integration with Martini force field

Dear Martini and GROMACS users, I am trying to perform thermodynamic integration on cg simulations using the Martini FF and GROMACS version 3.3.1 with double precision on a system containing a protein, lipids, water and Cl- ions. In the first test runs I tried to change the Martini atom type Qd

Re: [gmx-users] thermodynamic integration

Hi, > is it possible to do thermodynamic integration in Gromacs using non-linear > scaling of the lamda paramerter? I'm not sure exactly what you mean, so first I'll answer what I think you mean, and then tell you what I think you ought to be asking. :) If you mean, "Is it possible to perform a

[gmx-users] thermodynamic integration

Hi all , is it possible to do thermodynamic integration in Gromacs using non-linear scaling of the lamda paramerter? __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com