On Wed, Mar 29, 2006, James W wrote:
> My system is SAMs (self assemble mileculars) , 120 units
> (ASP-CYS-CYS-CCCCCCCCCCCCCCCCC / unit ).
It's not clear if you are simulation 1 unit (20 residues), or trying to
simulation 120 units (2400 residues). The latter would represent an enormous
calculation.
>
>
> I am confused about the
> kinetic energy and temperature . I set the value of "temp0" equil to
> 300.0 k .But when " NSTEP " is 700 ,
> I found that "TEMP(K) = 3107.84" .
You have no temperature regulation, and started from what is probably
a non-equilibrated structure (since you set irest=0). You are not even
approximately conserving total energy, which may arise because of bad
forces in the system. Are you starting from a minimized structure? How
were the initial coordinates determined?
Be sure you have some experience with an "ordinary" protein or nucleic acid,
before embarking on a project where the initial structure might not be known
so well.
...dac
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Received on Sun Apr 02 2006 - 06:10:09 PDT
