Subject: Re: "parallel" MD

From: [email-masked] (Klaus R. Liedl)
Date: Tue, 1 Nov 1994 11:24:35 +0100 (NFT)

Dear Noy,

Just a few hints to you:

1. It is trivial, that changing the sign of the time-coordinate
   is equivalent to changing the sign of the velocity coordinates
   in a CONSERVATIVE system (actually it is valid a little bit more
   general), as long as you remember that you have to sample with the
   "forward" velocities of your backward "simulation".

2. The problems you get with things like temperature bath, 
   Cutoffs, ... are just the same as in the forward direction.
   (You do not get trajectories in either direction.)

3. There is nothing like a "equilibrium" in a microcanonical ensemble ...
   (The process you call equilibration is just a complicated methode
   to find a starting point in phase-space. It has nothing
   to do with a trajectory or a simulation.)

4. You do not need ONE trajectory for your sampling. You can sample
   over as many trajectories as you like. The only problem is to find
   starting points for your trajectories (cf. 3.).  
   Even your methode in principle gives you ONE "MD-trajectory" (with the
   limitations of 2.) this is not the real point.  
   The time you save is not the time for the actual simulation, but the
   time for searching a second starting point in phase space. 

Good luck

Klaus
-- 
([email-masked])
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LinuX the choice of the GNU-generation

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From: Steve Stuart <[email-masked]>
Date: Tue, 1 Nov 1994 09:11:42 -0500

>   time for searching a second starting point in phase space. 

and a few other people have made similar comments, stating
that you could parallelize over N processors, if you could just find N
different starting points.

I just thought I'd point out that for many interesting properties
(diffusion constant, residence times, etc) the the total
length of the run can be more important than the number of runs
averaged over.  So it is important that the forward and backward
"trajectories" have the same starting point.

One other comment that interested me is K Bryson's note that the
reverse run would begin to unequilibrate the system.  (Now why didn't
that occur to me...)  Certainly true if you started from some ordered
state and never adjusted the temperature, but any T-scaling would
prevent this.  Out of curiosity - does anyone know how reversible a
non-T-scaling MD run actually is?  (with/without cutoffs, SHAKE,
whatever)

-Steve Stuart
[email-masked]

echo "a'rfg cnf Crpv | har" | tr '[a-m][n-z] ' '[n-z][a-m]\012' | sort | tr "\012" " " ; echo " "