sorry, I meant change maxcyc to 10 (I said nstlim, which is for MD)
On 9/25/07, Su Nwe <snwe001.gmail.com> wrote:
>
> This is my "modified" input file for minimization:
> initial minimisation of our structure
> &cntrl
> imin=1, maxcyc=2000, ntr=0, ntpr=5, ntmin=0, igb=6, ntb=0
> /
>
> This is the "modified" code that I typed in for minimization
> $AMBERHOME/exe/sander -O -i min_kelly.in -o min_kelly.out -p
> kelly.prmtop -c kelly.inpcrd -r min_kelly.rst
>
> But the restart (.rst) file is still not created. Can anyone help me
> please?
>
> Thanks in advance
> Su.
> On 9/25/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> > 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.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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> >
> >
> >
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Received on Wed Sep 26 2007 - 06:07:26 PDT
