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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Received on Fri Jan 22 2010 - 10:30:04 PST
