On Fri, 2014-03-14 at 12:03 +0530, Sushi Shilpa wrote:
> Dear Amber users
>
>
>
> I am facing some problem in restart files while doing production. I am
> running 1ns simulation and my input is like this
> production - GB - igb8 -
> &cntrl
>
> imin=0, irest=1,
> ntx=5,
> nstlim=500000,
> dt=0.002,
> ntc=2, ntf=2,
> igb=8,iwrap=0,
> ntpr=500, ntwx=500,
> ntwr=500,
> ntt=3,
> gamma_ln=2.0,
> temp0=300.0
>
> /
>
> Hold my protein name
> fixed
> 5.0
>
> RES 1
> 94
> END
>
> END
>
>
> but am getting errors like this if i go for further simulation using the
> previous rst
>
> I could not understand line 899 :
> ************ 870.6541615 -26.0313910-578.9666518 33.3247032-364.7185505
> *s in the inpcrd file often indicate an overflow of the Fortran format used
> to store coordinates in the inpcrd/restart files. This often happens when
> particles diffuse very far away from each other. Make sure you are removing
> center-of-mass translation (nscm /= 0) or check if you have multiple, mobile
> molecules that have diffused very far away from each other. This condition
> is
> highly unusual for non-periodic simulations.
> after that I have gone through amber discussion mail. And I gave the
> command iwrap=o but still am facing the same problem.
>
>
> Can anybody please advise on this regard
Read the error message carefully. Specifically:
"This often happens when particles diffuse very far away from each
other. Make sure you are removing center-of-mass translation (nscm /= 0)
or check if you have multiple, mobile molecules that have diffused very
far away from each other."
Visualizing your trajectory always helps. Furthermore, if you read the
description of the iwrap variable (both in the history of the Amber
mailing list and in the manual), it should be readily obvious why it has
no effect on your system (and why it only affects systems with periodic
boundary conditions). Taking the time to understand these things now
will drastically improve your understanding and productivity in the
future.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 14 2014 - 05:00:04 PDT
