2010/4/7 Yunfen Wang <wangfen041237.163.com>:
> Dear Jason,
> Thank you for your last instructions . Now , I have found the **** in the restart file ,and deleted the following lines from there . I re-run simulation , a new problem has appeared . In the Output there has another error:
> | Flags:
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
> | peek_ewald_inpcrd: Should not be here
> What's wrong? Should I delete content in other files while delete the **** in the restart file ?
You can't simply delete the lines with **** in your restart file. The
existence of a **** means that one of the coordinates for one of the
atoms is simply unknown, and you can't use the restart file at all.
You have to go back to a restart file that has no ***** in place of
coordinates (a different file!). (When you delete ****, the program
finds fewer coordinates than it is expecting to).
All the best,
Jason
> Expect your further instructions !
> Thank you
> Wang
>
>
>
> 在2010-04-07 22:00:05，"Jason Swails" <jason.swails.gmail.com> 写道：
>>Hello,
>>
>>Check your restart file for *****. This indicates that one of the
>>coordinates has become too large for the fixed-format form of the
>>restart file. If this is the case, you'll have to use your last
>>working restart file and re-run simulations from there. To avoid this
>>problem, use 'iwrap' in your input file. Details about this variable
>>can be found extensively in the archives as well as detailed in the
>>manual.
>>
>>Good luck!
>>Jason
>>
>>On Wed, Apr 7, 2010 at 9:56 AM, Yunfen Wang <wangfen041237.163.com> wrote:
>>> Dear users,
>>> When I run MD simulations, I often meet the follow Error and the simulation is stopped.
>>> The error : Sander bomb in subroutine nonbond_list
>>> volume of uncell too big ,too many subcells list grid memory needs to be reallocated ,restart sander
>>> when I meet it , I restart the input file and the running is continued But this time , I restart , it reminds the follow error and break the simulation
>>> The error :
>>> At line 2441 of file -ew -setup.f (unit9 "***.rst")
>>> Traceback: not available , complile with
>>> - ftrace = frame or - ftrace = full
>>> Fortran runtime error :bad value duiring floating point read
>>> I didn't know why . Is there anybody meeting the similar cituation ? Can give me advice ?
>>> Thank you in advance
>>> Reminding that I have checked the software and maked test , there was nothing wrong .
>>> Looking forward for your suggestions and instruction.
>>> sincerly,
>>> Wang
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>>--
>>---------------------------------------
>>Jason M. Swails
>>Quantum Theory Project,
>>University of Florida
>>Ph.D. Graduate Student
>>352-392-4032
>>
>>_______________________________________________
>>AMBER mailing list
>>AMBER.ambermd.org
>>http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 07 2010 - 21:30:02 PDT
