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 - 10:30:04 PST
