[Xplor-nih] IVM and PARArestraints problem

[Charles at Schwieters.org]

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Hello Tiandi--

>   Since the structure of the protein and the tag are
> known, we want to group them during the simulation but
> not fix them. I know IVM (Dynamic Internal) is good
> for dealing this kind  of problem. And PCS will be
> used so I modify the script downloaded from
> Dr.Bertini's website. The problem is that the
> structures generated by this script are identical.

This is probably due to the fact that the velocities are not randomized
before the high temperature dynamics. To randomize velocities, add the
lines
      vector do (vx = maxwell($init_t)) (all)  
      vector do (vy = maxwell($init_t)) (all) 
      vector do (vz = maxwell($init_t)) (all) 

before the first dynamics internal statement. Note also that IVM
topology is maintained between calls to dynamics internal, unless a
reset statement is specified.

best regards--
Charles
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