AMBER Archive (2003)

Subject: PME

From: Yuguang Mu (ygmu_at_theochem.uni-frankfurt.de)
Date: Tue Jun 10 2003 - 07:04:08 CDT

Dear David,
I try to install AMBER force field to another MD program,e.g. GROMACS.
When I compare two results,one from original AMBER, one from GROMACS,
in the case of vacuum, cutoff, I got complete same results.

But when I use PME, the results do differ. Mainly in the energy terms
of electrostatics.

I remember that in AMBER there are other switches related with PME,
for example, VDWMETH. DO you think these kinds of switches can effect
the simulation results greatly ?

Do you think which system can be reliabley used to check such
force field implimentations ?

Thanks

Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711

On Tue, 10 Jun 2003, Bimo Ario Tejo wrote:

> Thanks Dr. Yuguang,
>
> Unfortunately, my output trajectory is coordinates file, not velocity. Is it another way to observe the helix/domain movement quantitatively without velocity information? FYI, the helix creates a flap over the protein which is open and closed during catalysis.
>
> Best wishes,
>
> Bimo
> ITB - Stutgart
>
> ----- Original Message -----
> From: Yuguang Mu <ygmu_at_theochem.uni-frankfurt.de>
> Date: Tue, 10 Jun 2003 12:47:42 +0200 (MEST)
> To: Bimo Ario Tejo <bimo7_at_linuxmail.org>
> Subject: Re: helix movement
>
> > My rough idea is following :
> > get coordinates and velocities of the helix/domain
> > then calculate the exectly the overall translational and rotational
> > velocities. then you may have a idea of such movement.
> >
> > Dr. Yuguang Mu
> > Institute for Physical and Theoretical Chemistry
> > J.W. Goethe University Frankfurt am Main
> > Marie Curie Str. 11
> > 60439 Frankfurt/Main, Germany
> > Tel: +49-(0)69-798-29711
> >
> > On Tue, 10 Jun 2003, Bimo Ario Tejo wrote:
> >
> > > Dear Amber users,
> > >
> > > Does anyone have a tool to calculate the movement of helix and/or domain from Amber trajectory file? Superimposing some snapshots is useful, but it is not a quantitative way to describe such a movement.
> > >
> > > Any help is highly appreciated.
> > >
> > > Best regards,
> > > Bimo
> > > ITB - Stuttgart
> > > --
> > > ______________________________________________
> > > http://www.linuxmail.org/
> > > Now with e-mail forwarding for only US$5.95/yr
> > >
> > > Powered by Outblaze
> > >
> > >
> >
>
> --
> ______________________________________________
> http://www.linuxmail.org/
> Now with e-mail forwarding for only US$5.95/yr
>
> Powered by Outblaze
>