Re: [AMBER] heat further an equilibrated system

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 22 Jan 2010 13:28:25 -0500

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
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