[gmx-users] more frames...
spoel at xray.bmc.uu.se
Thu Feb 27 20:25:36 CET 2003
On Thu, 2003-02-27 at 18:59, Giorgos Karvounis wrote:
> On Wed, 2003-02-26 at 22:40, Giorgos Karvounis wrote:
> > > Even so, i will never be able to reproduce exactly the same
> > coordinates and velocities with my original run , since i am using
> > T-coupling , am i right? I am trying to reproduce , if possible,
> > the same run, just with more frames. It seems that it starts off with
> > the same coordinates and velocities but after some time, the box size
> > coordinates and velocities deviate from my original run.I assume that
> > this is due to T and P coupling but i am not sure.Is it possible in
> > way to reproduce exactly the same run?
> Not right now without hacking the code. It can be done in principle by
> storing an extra frame of velocities. (at time t, and t-delta t)
> Dear all,
> >From what i understood from David's answer, the only way that i can
> reproduce exactly the same run is to hack the code. I am happy to do
> that since it is very important to me to regenerate the same coordinates
> and velocities with my original run (not starting from the begining but
> starting from a frame). But its not so clear to me what to hack and why.
> I though the problem was on T/P coupling. So how will i be able to sort
> this by storing an extra frame of velocities at time t ,and t-delta t?
first, check the algorithm, how the velocities at
v(t) = 1/2 * [ v(t-dt/2) + v(t+dt/2) ]
basically, you have to store two velocity frames, and read them in again
at the start of mdrun.
Start by reading the manual if you haven't already, then check the
calc_ekin routine in update.c.
If you still want to continue doing it then let's move this discussion
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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