AMBER Archive (2007)

Subject: AMBER: Minimization and MD input files

From: Su Nwe (snwe001_at_gmail.com)
Date: Tue Sep 25 2007 - 13:23:49 CDT

Dear Amber users

I'm trying to run a simple molecular dynamic "without solvent" on an
organic molecule using Amber 9. I could neither do minimization nor
molecular dynamics. I'm assuming that I made some errors in setting
parameters.

The following is my minimization input file.
initial minimisation
&cntrl
  imin=1, maxcyc=2000, ntr=0, ntpr=5, ntmin=0, igb=0
 /

After minimization, .rst file wasn't created.

This is my molecular dynamic input file.
300K constant temp MD
 &cntrl
  imin=0, ntb=1,
  ntc=2, ntf=2,
  tempi=300.0, temp0=300.0,
  ntt=3, gamma_ln=1.0,
  nstlim=1000, dt=0.002,
  ntpr=1, ntwx=1,
 /

I tried running the system "with solvent". Both minimization and
molecular dynamic works, but when I looked at the molecule (.mdcrd
file) using VMD, the molecules were shooting out everywhere and moving
so randomly.

Can someone please help me figure out what I'm doing wrong or give me
some comment on my input files.

Thanks in advance

Sincerely,
Su.
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