AMBER Archive (2007)

Subject: Re: AMBER: Minimization and MD input files

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Sep 25 2007 - 13:30:17 CDT

what does sander say in the output file from the minimization?
note that igb=0 does not mean "no solvent", it sets a periodic
system. you might try igb=6.

On 9/25/07, Su Nwe <snwe001_at_gmail.com> wrote:
>
> 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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