Thank you for suggestions bill.
Thanks & Regards
Sneha Rai
Ph.D. Research Scholar
Computational and Structural Biology Lab
Division of Biotechnology
NSIT
On Thu, May 12, 2016 at 2:07 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Doubly sorry, I was going on the documentation, which is ambiguous at
> best on the default for ioutfm - it seems to be ascii after all, as seen
> in my own simulation. So please try 'tail mdcrd' etc.
>
> Bill
>
>
> On 5/12/16 1:33 AM, Bill Ross wrote:
> > I'm sorry, unless you have an old version of Amber, your mdcrd should be
> > binary, and coordinate overflow would be less likely to be an issue. Can
> > you compare the size of the mdcrd to that of another run? Does the mdout
> > show normal termination?
> >
> > Bill
> >
> >
> > On 5/12/16 1:21 AM, Bill Ross wrote:
> >> If you inspect by e.g. 'tail mdcrd' or 'less mdcrd', do you see any ***
> >> or numbers that run together?
> >>
> >> Bill
> >>
> >>
> >> On 5/12/16 1:18 AM, Sneha Rai wrote:
> >>> Dear Amber users,
> >>>
> >>> I have used the following input file for 20 ns production run. The
> output
> >>> file indicates that run is complete without any errors. However, when I
> >>> load mdcrd file of production run in VMD, only 1367 frames were loaded
> and
> >>> I was expecting 4000 frames. Following is my input file for production
> run,
> >>> kindly suggest possible solution for this problem.
> >>>
> >>> Production
> >>> &cntrl
> >>> imin=0,
> >>> ntx=5,
> >>> irest=1,
> >>> nstlim=10000000,
> >>> dt=0.001,
> >>> ntf=2,
> >>> ntc=2,
> >>> temp0=300.0,
> >>> ntpr=2500,
> >>> ntwx=2500,
> >>> ntwr=2500,
> >>> cut=8.0,
> >>> ntb=2,
> >>> ntp=1,
> >>> ntt=3,
> >>> gamma_ln=2.0,
> >>> /
> >>>
> >>>
> >>> Thanks & Regards
> >>>
> >>> Sneha Rai
> >>> Ph.D. Research Scholar
> >>> Computational and Structural Biology Lab
> >>> Division of Biotechnology
> >>> NSIT
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Received on Thu May 12 2016 - 02:30:04 PDT
