AMBER Archive (2003)

Subject: AMBER: MD problem!!

From: Pradipta Bandyopadhyay (pradipta_at_cgl.ucsf.edu)
Date: Thu Sep 18 2003 - 15:35:36 CDT

 Sorry, I should have been more concrete.

 After generating the 256 waters in Leap, I am doing

 (1) 1500 steps of minimization (250 steepest descent steps) with SHAKE.
 (2) Series of short NVT simulations to heat up the system to 300K
     total time 40 pico second.
 (3) Then I tried NPT but the run crashes, the density was about 0.82.

     Following the suggestion of Dr. Darden, I reduced the box size by
     ~ 1% and then 2.5 pico second NVT and checked density.
     After doing this 8 times, I get a density about 0.959.

     However, NPT simulation from that crahses after 0.24 picosecond.

  I don't mind running it longer only if it doesn't crash. There are few
waters a bit far from the rest - may be these are causing problems.
My step size was 1 fs and it is all AMBER7.

I can send the input files. I haven't used AMBER for a while - may be some
input parameters are not appropriate.

thanks.

         Pradipta

> taking very long time to equilibrate. Is there a better way?

>> How long did it take to equilibrate? How long do you expect it should
>> take?
>> I just like to have a bit of sense on how long is "very long" for you
>> (people may have different standards).

>> yong

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