Hi Jason,
I have included the restraint information. It is running now. Thank you for the help.
Jaya.
On 01/22/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> Your problem is that your input file contains no restraint
> information. You need to include a "restraintmask" and
> "restraint_wt". When you do this, your simulation should work.
>
>
> Good luck!
> Jason
>
> On Fri, Jan 22, 2010 at 1:17 PM, Jayalakshmi Sridhar <jsridhar.xula.edu> wrote:
> > Here is my md.in file:
> > 2A6 protein from 1Z10:
> > &cntrl
> > imin = 0,
> > irest = 1,
> > ntx = 5,
> > ntb = 1,
> > cut = 10,
> > ntr = 1,
> > ntc = 2,
> > ntf = 2,
> > tempi = 300.0,
> > temp0 = 350.0,
> > ntt = 3,
> > gamma_ln = 1.0,
> > nstlim = 20000, dt = 0.002
> > ntpr = 200, ntwx = 200, ntwr = 2000
> > /
> >
> >
> >
> > On 01/22/10, Jason Swails <jason.swails.gmail.com> wrote:
> >>
> >> On Fri, Jan 22, 2010 at 12:57 PM, Jayalakshmi Sridhar <jsridhar.xula.edu> wrote:
> >> > Sorry about that. The university webmail I am using keeps changing the options frequently. I have now tried to send it again as plain text. Hope it comes out ok. The problem I am encountering is this:
> >> > When reading the reference coordinates it says-
> >> > rfree: End of file on unit 5.
> >>
> >> unit 5 should be the mdin file. the refc file should be unit 10, so
> >> the problem, I think, lies in the mdin terminating sooner than the
> >> program expects it to.
> >>
> >> This is not indicative of erroneous input values necessarily, but
> >> rather an incorrectly assembled namelist. What does your input file
> >> look like?
> >>
> >>
> >> --
> >> ---------------------------------------
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Graduate Student
> >> 352-392-4032
> >>
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> >>
> >
> >
> >
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>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
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Received on Fri Jan 22 2010 - 11:00:02 PST
