You can't. (And it probably wouldn't be meaningful if you could,
since, for example, the change in the protein-protein interactions
depends on what the water and ligand are doing).
David
On 7/24/07, Georgios Patargias <[EMAIL PROTECTED]> wrote:
Thanks once more for your reply David.
Do you know by any chance if we can get the dVpot/dlambda
for one of the default group of atoms (e.g. protein) rather than
for the whole system?
Best wishes
George
Dr. George Patargias
Polymer IRC Group
University of Leeds
Leeds, LS2 9JT, UK
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of David Mobley
Sent: Tue 7/24/2007 5:00 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] FEP and soft-core potentials
Right. In fact, usually you would lose efficiency by using soft core
potentials for an electrostatic transformation over doing it without
soft core. The purpose of soft core is just to fix the problem with
disappearing/inserting atoms which have 1/r^12 repulsion.
David
On 7/24/07, Georgios Patargias <[EMAIL PROTECTED]> wrote:
> Hello
>
> Just a quick question about Free Energy Pertubation simulations. Do I
understand
> correctly that if the only thing that changes from State A to B is the
partial charge
> of a single atom, then I don't need the soft core potentials?
>
> Thanks.
>
> Best wishes
> George
>
>
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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 [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
