[gmx-users] mutation FE calculation with oplsaa

[Qiang Li]

Dear all users,

1,
I am modifying the .top file for mutation free energy calculation(A->B), so
I need the provide the parameters of structure A and B in [bonds], [angles],
[dihedrals].
Is it possible for me to provide only the parameters of B but le the grompp
using the default parametes of initial structure A?

I know the A parameters will be copied to B if parameters of B is not
explicitly defined in .top. IS that means I must explicitly define both A
and B at the same time?
I ask it since I find in OPLSAA force field the .top file does not contain
paramters of [bonds], [angles],... but only the atome numbers and function
types.

2,
When comparing the solvation free energy tutorial from
http://md.chem.rug.nl and
the wiki(Dillgroup), I get confused at the definition of solvation free
energy.
In the former, dG=dG1(in vacuo)-dG2(in water); however, in the latter it
seems only calculating the dG2(in water) gives excellent result compared to
expt.
Did I misunderstand anything here?

thanks a lot

LQin
___
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 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

Re: [gmx-users] mass changes in free energy calculations

[Qiang Li]

Thanks for clearing the doubt.

Is that more easier to get equlibrium to use unchanged mass when doing LJ
turning on/off?
I ask this since I found the forwards and backwards mutation free energy are
more consistant if I do not change the mass. Accidentally?

LQ

On Thu, Jun 19, 2008 at 4:26 AM, David Mobley <[EMAIL PROTECTED]> wrote:

> You can change the mass if you like. Basically, the net free energy
> change associated with changing the mass should end up being zero so
> it will be irrelevant. The mass of course affects the dynamics and
> things like the velocities, but based on equipartition you can
> convince yourself that the free energy change will be zero.
>
> David
>
> On Fri, Jun 13, 2008 at 12:04 AM, friendli <[EMAIL PROTECTED]> wrote:
> > Dear all,
> >
> > I am calculating FE using TI. I have a question about mutating existing
> > atoms with different mass.
> > for example, using ffG53a6 force field, in one case i need to mutate CH2
> to
> > CH3,
> > should I use
> > [ atoms ]
> > 17CH3  2ALA CB  6  0 15.035 CH2
>  0
> >14.027; qtot 1
> >
> > OR
> >
> > 17CH3  2ALA CB  6  0 15.035 CH2
>  0
> >15.035; qtot 1
> >
> > I notice from Prof. Alan Mark's online FE course, he mutates a H atom to
> a O
> > atom, but does not change its mass.
> > The line is :
> > 12HC1 PHE   HZ  6   0.11.008
> >   OA -0.54811.008
> >
> > Can somebody explain a bit why we should not change the mass accordingly?
> >
> >
> > thank you
> >
> > LQ
> >
> > I though I sent this email but why I can not see it. There may be
> something
> > wrong with my email software. so I send here again. sorry
> > ___
> > 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
> 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 listgmx-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 listgmx-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