[gmx-users] more frames...

David 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,
> exactly
> > 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
> any
> > 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
to gmx-developers

Groeten, David.
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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