trajectory file

Eckhard Hofmann eckhard.hofmann at uni-konstanz.de
Thu Jan 22 06:29:57 EST 1998


I'd like to get one trajectory file of a comlete MD Simulation from
3000K down to 500K. 
During the dynamics I can only write to a new file (is that correct?),
so each time the bath temperature is changed in the outer cycle, I have
to start a  new file.
I'am not clear about the way I can merge these different trajectories
into one big file. I guess the problem is that all files will start at
the same cycle (10 in this case) and end at 500. Does the numbering (in
the file) have to be different for the merging?
I'll attach parts of the inputfiles below.
Thanks for any hints,
Eckhard


slowcooling: (init 3000 ,cooling 500)
...
    evaluate ($1=$init_temp)
    while ($1 > 300.0) loop main     
      evaluate ($traj_name = "slow_mod"+encode($1)+".dcd")          
      dynamics  verlet 
         timestep=0.0005            
         nstep=500
         iasvel=current 
         nprint=0  iprfrq=0
         tcoupling=true tbath=$1   
       asci=false
       nsavc=10 
       traj=$traj_name
       end                                         
       evaluate ($1=$1-$cool_rate)
....
 

merging:

 {===>} structure @generate_mod.psf end       {*Read structure file.*}

dynamics merge
    asci=false
    input=slow_mod3000.dcd
    input=slow_mod2500.dcd
    input=slow_mod2000.dcd
    input=slow_mod1500.dcd
    input=slow_mod1000.dcd
    input=slow_mod500.dcd
BEGIn=      10  SKIP=      10  STOP= 500 
    output=slowmod.dcd
end

output merging:

.....
 X-PLOR>dynamics merge 
 MERGE>    asci=false 
 MERGE>    input=slow_mod3000.dcd 
 ASSFIL: file slow_mod3000.dcd opened.
 MERGE>    input=slow_mod2500.dcd 
 ASSFIL: file slow_mod2500.dcd opened.
 MERGE>    input=slow_mod2000.dcd 
 ASSFIL: file slow_mod2000.dcd opened.
 MERGE>    input=slow_mod1500.dcd 
 ASSFIL: file slow_mod1500.dcd opened.
 MERGE>    input=slow_mod1000.dcd 
 ASSFIL: file slow_mod1000.dcd opened.
 MERGE>    input=slow_mod500.dcd 
 ASSFIL: file slow_mod500.dcd opened.
 MERGE>BEGIn=      10  SKIP=      10  STOP= 500 
 MERGE>    output=slowmod.dcd 
 MERGE>end 
 ASSFIL: file slowmod.dcd opened.
 REMARKS FILENAME="slow_mod3000.dcd"
 REMARKS file xtallib/scatter.lib
 REMARKS Atomic scattering factors without anomalous contribution
 REMARKS Library for X-PLOR(online)
 REMARKS
 REMARKS Authors: Paul Adams, Joe Jaeger, and Axel T. Brunger
 REMARKS DATE:21-Jan-98  15:53:16       created by user: ecki
 READC: reading file=   1   ISTART=      10
 READC:     1432 atoms were "free"
 READC: NUNIt=   6
 READC: BEGIn=      10  SKIP=      10  STOP=     500
 READC: TIMEstep=  0.00050000 ps    header= CORD
 WRITEC: CORD sets starting from step       10 are written every    10 
steps
 WRITEC: where     1432 atoms are "free"
 READC: complete.       50 coordinate sets were passed to calling
routine
 X-PLOR> stop 
 



-- 
Eckhard Hofmann           <eckhard.hofmann at uni-konstanz.de>
Fakultaet fuer Biologie
Universitaet Konstanz
Box M656
D-78457 Konstanz, Germany
Phone: voice: +49 7531 88-2211   fax: +49 7531 88-3183



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