Dr. Kallies: Please send questions concerning amber to the mailing list
<amber_at_heimdal.ucsf.edu> rather than to me personally. I am forwarding
this to that list, where I know there are people (like Carlos Simmerling
and Tom Cheatham) who have been thinking recently about this very problem.
..regards...dac
On Mon, Jul 09, 2001, Bernd Kallies wrote:
> I have a probably simple question regarding a piece of AMBER code (rel.
> 5.0.1, runmd.f) that I do not understand. It is commented as "Step 8"
> and removes translational and rotational motions of the center of mass
> for non-periodic simulations:
>
> DO I3 = 1,NR2
> F(I3) = X(I3)-V(I3)*DT5
> enddo
> CALL CENMAS(NRP,IZERO,F,V,...)
> DO I3 = 1,NR3
> X(I3) = F(I3)
> enddo
> CALL STOPCM(NR,X,V,...)
> CALL CENMAS(NRP,X,V,...)
>
> To my opinion at this time the array V stores the velocities v(t + dt/2)
> and the array X stores the coordinates x(t + dt) according to the
> leap-frog Verlet algorithm ready for the next MD step. The first lines
> obviously implement some kind of Taylor expansion of X and put the
> result into F. To my opinion it should hold X(t + dt/2) in order to
> synchronize X and V when calling CENMAS. If so, then it should calculate
> X(t + dt/2) = X(t + dt) - V(t + dt) dt/2 or alternatively = X(t) + V(t)
> dt/2, but not = X(t + dt) - V(t + dt/2) dt/2 as it seems to do. And why
> is X(t + dt/2) from F after the first call of CENMAS taken as new X? I
> think it should still hold X(t + dt) for the next MD step?
>
> Thanks in advance, B. Kallies
>
> --
> Dr. Bernd Kallies
> Institute of Physical and Theoretical Chemistry
> University Potsdam
> 14476 Golm
> Karl-Liebknecht-Str. 24-25
> Tel: ++49 / 331 / 977 - 5372
> Fax: ++49 / 331 / 977 - 5058
> Mail: kallies_at_chem.uni-potsdam.de
> WWW: http://www.chem.uni-potsdam.de/~kallies/
>
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Mon Jul 09 2001 - 08:06:21 PDT
