Hello,
I have used iwrap = 1 during the whole simulation already, and also appeared the trouble
Thanks
Wang
在2010-04-08 18:36:24，"Trevor Gokey" <tgokey.sfsu.edu> 写道：
>
> Hello,
> I am currently dealing with a nearly identical issue so = maybe I can help.
> It's not very clear whether you used iwrap or not, but th= e good way to go
> seems to be to run a single step using iwrap = 1 with nt= wr = 1 so that
> you get a valid restart file. I got *** in my restart file= s because the
> numbers were greater than 1000, meaning the waters have wande= red too far
> away. Using iwrap brings these waters back, and in my case the = numbers
> were -30 < x < 30, which gives plenty of time before they wan= der too far
> off again and you need to use iwrap again.
> Jason: You sa= id that one must revert back to the last valid restart file
> if the coordina= tes >= 1000. However, is there controversy to modifying
> these numbers = in the restart file to 990 if it is known that the actual
> values are fairly= close to 1000? I generated an equivalent restart file
> from ptraj (which ou= tputs coordinates >=1000) and I found 3 of them to
> be ~1080. I then to= ok this and used iwrap for a step and then went back to
> my normal routine. = However, I was initially concerned that this would
> affect the density of th= e system, but mdout is reporting consistent
> densities. Why is this so?
> <= br>Hope this helps, Wang.
>
> -----[1]= <amber-bounces.ambermd.org> wrote: -----
> To: amber [2]<amber.ambermd.org><= /a>
> From: Yunfen Wang [3]<wangfen041237.163.com>
> Sent by: <= a class="moz-txt-link-rfc2396E"
> href="mailto:amber-bounces.ambermd.org"= ><amber-bounces.ambermd.org>
> Date: 04/08/2010 03:05AM
> Subje= ct: [AMBER] Fortran runtime error :bad value duiring floating point
> read
> Dear users,
> For MD simulations , I often meet the follow Error :
> = ; "Sander bomb in subroutine nonbond_l= ist
> volume= of uncell too big ,too many subcells list
> &= nbsp; grid memory needs to be reallocated= ,restart
> sander"
> Whenever I met it , I just re-run the simulation by re= starting the input
> file and it continued .
> But this time, it can't conti= nue but the follow Error:
> = ; "At line 2441 of file -ew -setup.f (unit9 "***.rst")
> &nb= sp; Traceback:= not available , complile with
> = - ftrace = frame or - ftrace = full
> = ; Fortran runt= ime error :bad value duiring floating
> point read"
> I found "****"in the r= estart file .As Jason says, I should re-run the
> simulation . However,= when I re-run the MD simulation using my last working
> restart file , = ;it crashed at the same time "ns", reminding the first
> Error , and re-run w= ith the second Error . I likely cann't jump out the
> problem.
> Shoul= d anyone give me any instructions and advice ï¼
> Looking for= ward for your answersï¼ Thanks in advance !
> sincerly,
> Wang_____ _________________________ _________________
> AMBER mailing list[4]A= MBER.ambermd.org
> [5]http://lists.ambermd.org/mailman/listinfo/amber
> Trevor
>
>References
>
> 1. 3D"mailto:amber-bounces.ambermd.org"
> 2. 3D"mailto:amber.ambermd.org"
> 3. file://localhost/tmp/3D"ma 4. 3D"mailto:AMBER.ambermd.org"
> 5. 3D"http://lists.ambermd.org/mailman/listinf_______________________________________________
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Received on Thu Apr 08 2010 - 05:30:02 PDT
