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 ？
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"
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Received on Thu Apr 08 2010 - 04:00:02 PDT
