Rebeca,
You can keep the previous mdcrds and restarts until now, and post
process everything with ptraj.
However, there will me some numerical errors (accuracy) associated with
that wrapping back into the main box.
We have done this before and has never come back to bite us, but it is a
potential problem.
Tom Cheatham might comment on this.
rebeca.mmb.pcb.ub.es wrote:
> Thanks a lot for your suggestion,
> as you mention the restart file sander have several **** instead of a
> number,
> so that must be the cause of the problem. I will try iwrap=1.
>
> Only one more question, should I restart all the simulation, or could I
> begin to
> use iwrap=1 just from now on, from the simulation that has failed, and
> mantain
> the older ones with iwrap=0? Will ptraj post-processing will correct this
> mixture and change translating molecules back to the primary box?
>
> Thanks again for you help,
>
> Rebeca García Fandiño
> Parc Cientific de Barcelona
> Barcelona
> rebeca.mmb.pcb.ub.es
>
>
> Quoting Martin Klefas-Stennett <martin.stennett.postgrad.manchester.ac.uk>:
>
>> I found that this was caused when some of the atom positions became
>> too large to fit into the width of the output field assigned to them.
>> When writing the restart file sander had written ***** instead of a
>> number and when it re-imported the data I got the same messages as you.
>> My problem was cured by using iwrap=1 in all of my runs.
>>
>> Martin
>> rebeca.mmb.pcb.ub.es wrote:
>>> Dear Amber users,
>>>
>>> I am having troubles with several AMBER calculations. Some of them
>>> finish with
>>> an error (in the error file) of the type of:
>>>
>>> 1525-097 A READ statement using decimal base input found the invalid
>>> digit '*'
>>> in the input file. The program will recover by assuming a zero in
>>> its place.
>>> 1525-097 A READ statement using decimal base input found the invalid
>>> digit '*'
>>> in the input file. The program will recover by assuming a zero in
>>> its place.
>>> 1525-097 A READ statement using decimal base input found the invalid
>>> digit '*'
>>> in the input file. The program will recover by assuming a zero in
>>> its place.
>>> (...)
>>> srun: error: s05c5b05: task[8-11]: Segmentation fault
>>> srun: Job Failed
>>>
>>> The input file is OK, since I have used it for the previous simulations:
>>>
>>> &cntrl
>>> imin=0,
>>> irest=1,
>>> ntx=7,
>>> ntb=2,
>>> cut=10,
>>> pres0=1.0,
>>> ntp=1,
>>> taup=2.0
>>> ntr=0,
>>> ntc=2,
>>> ntf=2,
>>> tempi=300.0,
>>> temp0=300.0,
>>> ntt=3,
>>> gamma_ln=0.1,
>>> nstlim=700000,
>>> dt=0.002,
>>> ntpr=1000,
>>> ntwx=1000,
>>> ntwr=1000
>>> /
>>>
>>> I am using Amber 9.0 and this error has appeared in several
>>> simulations that do
>>> not have anything to do between them.
>>>
>>> Has any of you had this type of problem in your simulations?
>>>
>>> Thanks a lot for your help in advance,
>>>
>>>
>>> Rebeca García Fandiño
>>> Parc Cientific de Barcelona
>>> Barcelona
>>> rebeca.mmb.pcb.ub.es
>>>
>>>
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber.scripps.edu
>>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>>
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project and Department of Chemistry
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
============================================================================
To announce that there must be no criticism of the president,
or that we are to stand by the president right or wrong,
is not only unpatriotic and servile, but is morally treasonable
to the American public."
-- Theodore Roosevelt
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Nov 14 2007 - 06:07:28 PST
