Re: [AMBER] Fortran runtime error :bad value duiring floating point read

From: Trevor Gokey <>
Date: Thu, 8 Apr 2010 03:36:24 -0700

   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]= <> wrote: -----
   To: amber [2]<><= /a>
   From: Yunfen Wang [3]<>
   Sent by: <= a class="moz-txt-link-rfc2396E"
   href=""= ><>
   Date: 04/08/2010 03:05AM
   Subje= ct: [AMBER] Fortran runtime error :bad value duiring floating point
   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
   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
    Shoul= d anyone give me any instructions and advice ´╝Ÿ
    Looking for= ward for your answers´╝ Thanks in advance !
   Wang_____ _________________________ _________________
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Received on Thu Apr 08 2010 - 04:00:02 PDT
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