[gmx-developers] hacking the update algorithm

Erik Lindahl lindahl at stanford.edu
Fri Mar 7 00:11:17 CET 2003

Hi Giorgios,

David is on vacation right now, and since I haven't read your previous 
discussion in detail it is probably best to repost this in a week when 
he's back!



On Thursday, Mar 6, 2003, at 12:32 US/Pacific, Giorgos Karvounis wrote:

> Dear developers,
> i would like to hack the update algorithm in order to reproduce the
> exactly the same run  "b"  from an original run "a" but starting from a
> random frame of the original run (i.e. not from the first step). If my
> original run was without T and P coupling , i can always reproduce it,
> at any time frame. First of all some general questions:
> 1) From previous answers , i get the impression that this is happening
> due to T coupling only (although P coupling rescales co-ordinates and
> box-size!). I tried to reproduce a run without T but with P coupling 
> and
> i couldnt do it ( gen_vel=no, unconstrainstart=yes e.t.c), maybe need 
> to
> change something else at the mdp file?
> 2) When i take a random frame from my original run using the same
> velocities v(t) (grompp -t .trr   -time...), i have the velocities at
> v(t). And this is an average of v(t-dt/2) and v(t+dt/2). I was 
> wondering
> if there is a problem there (as David suggested already that i need to
> store the velocities of v(t) and v(t-dt))  because i assume that the
> scaling factor will use the v(t-dt/2) to get the Ekin(t-dt/2) and from
> there to get the T  at t-dt/2 ...or maybe not? Is this the reason why 
> we
> cannot reproduce the same run with T coupling?
> 3)I was also wondering, if i put a switch to the code , and turn the
> coupling (T and/or P) off at the frames that i want (eg every 20000
> steps) will this do the trick?
> 4) At the end of the day, is it worth to get to all this trouble 
> instead
> of making  a short 'equilibration' run and then continue the rest of my
> simulation (2ns) without T/P coupling (some kind of NVE simulation)? So
> far i used weak coupling and i dont know if it would be reasonable to 
> do
> without.
> If you are not already dizzy, and if any of this makes sense, thanks!
> :-)
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