Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame

From: Jason Swails <>
Date: Thu, 8 Apr 2010 08:51:34 -0400

By using iwrap, you mean set iwrap=1 in your input file? If you use
iwrap, this problem should not occur, since particles are not allowed
to diffuse to such far locations... The only problem I can see with
this is if you don't have periodic boundary conditions (i.e. ntb=0),
and if you have free particles (like ions, for instance) that are
diffusing away from the rest of your system (since even with implicit
solvent/gas phase, the COM translation is eliminated every X number of
steps according to nscm.

All the best,

2010/4/8 Yunfen Wang <>:
> Jason,
>  I have tried that before ,but when running to the same ''ns'', it met the same trouble ! And also , I have used ''iwrap'' in my input file
> Thank you
> Wang
> 在2010-04-08 12:03:31,"Jason Swails" <> 写道:
>>2010/4/7 Yunfen Wang <>:
>>> 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,
>>> Expect your further instructions !
>>> Thank you
>>> Wang
>>> 在2010-04-07 22:00:05,"Jason Swails" <> 写道:
>>>>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
>>>>Good luck!
>>>>On Wed, Apr 7, 2010 at 9:56 AM, Yunfen Wang <> 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
>>>>Jason M. Swails
>>>>Quantum Theory Project,
>>>>University of Florida
>>>>Ph.D. Graduate Student
>>>>AMBER mailing list
>>> _______________________________________________
>>> AMBER mailing list
>>Jason M. Swails
>>Quantum Theory Project,
>>University of Florida
>>Ph.D. Graduate Student
>>AMBER mailing list
> _______________________________________________
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Apr 08 2010 - 06:00:04 PDT
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