Re: restarting Gaussian accelerated MD fails

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue Jan 22 2019 - 02:56:58 CST

Dear David, Dear all,

I am still having this problem when trying to restart gaussian aMD
simulations in NAMD 2.13. I sent you sometime ago all files to reproduce
the problem.

I also have a question regarding the k0 values. During the gAMD
equilibration, these values are updated at each time step whereas during
a production run , k0 is maintained constant throughout the simulation
..  That is correct, right ?

Now, what I noticed is that if I run a production run for 25 million
steps after 5 million equilibration phase, the restart file ".gamd"
after 25 million steps has on the second column "5000000" ... As his is
the step, it should be 25000000 .. Is it possible that the issue is
actually because of the program not being able to properly read this
restart file ?

Thanks for any advice on how to fix this issue ...

Best wishes
Vlad

On 8/9/18 5:26 PM, Vlad Cojocaru wrote:
> Dear David,
>
> Thanks a lot for offering to try to reproduce our problem with the
> gamd restart. I will send to you in a separate email, all files needed
> via "Cryptshare"
>
> Password to download is: "gamdrestart4vlad"
>
> the relevant NAMD configuration file is *gamd0102.conf ... For the
> record I also included the configuration file for the successful
> initial run (gamd0101) as well as the files with the error messages.
>
> If you have any questions please let me know
>
> Best wishes
> Vlad
>
> On 08/08/2018 06:35 PM, David Hardy wrote:
>> Dear Vlad,
>>
>> If you could off-list send me or direct me to system files that
>> reproduce this error, I will take a closer look next week when I'm
>> back at the office.
>>
>> Best regards,
>> Dave
>>
>> --
>> David J. Hardy, Ph.D.
>> Beckman Institute
>> University of Illinois at Urbana-Champaign
>> 405 N. Mathews Ave., Urbana, IL 61801
>> dhardy_at_ks.uiuc.edu <mailto:dhardy_at_ks.uiuc.edu>,
>> http://www.ks.uiuc.edu/~dhardy/ <http://www.ks.uiuc.edu/%7Edhardy/>
>>
>>> On Aug 3, 2018, at 4:58 PM, Miao, Yinglong <miao_at_ku.edu
>>> <mailto:miao_at_ku.edu>> wrote:
>>>
>>> Dear Vlad,
>>>
>>> We haven’t seen such problem so far, but I’m CC’ing Andrew Pang, who
>>> coded GaMD in NAMD, to see whether he can perhaps help with this …
>>>
>>> All the best,
>>> Yinglong
>>>
>>> Yinglong Miao, Ph.D.
>>> Assistant Professor
>>> Center for Computational Biology and
>>> Department of Molecular Biosciences
>>> University of Kansas
>>> http://miao.compbio.ku.edu <http://miao.compbio.ku.edu/>
>>>
>>>> On Aug 3, 2018, at 7:00 AM, Vlad Cojocaru
>>>> <vlad.cojocaru_at_mpi-muenster.mpg.de
>>>> <mailto:vlad.cojocaru_at_mpi-muenster.mpg.de>> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> We are trying to run some Gaussian accelerated MD simulations using
>>>> the NAMD CVS code from July 12 2018. First run when including some
>>>> initial classical MD and equilibration steps runs fine ... However,
>>>> when trying to restart after first run, we always get an error :
>>>> "error: co2141: task 0: Floating point exception" ...
>>>>
>>>> This is very cryptic and comes from the compute nodes and there is
>>>> no other error message, the NAMD output stops being written without
>>>> any message.
>>>>
>>>> Now, I know this is not much information but its hard to provide
>>>> all data needed to reproduce this in this email. That is why I
>>>> would like to ask if anyone has encountered this problem before. If
>>>> yes, is this is known issue which has a solution already ? If not,
>>>> is anybody willing to look at our inputs and see if there is
>>>> anything we are doing wrong ?
>>>>
>>>> Thanks for reading and for any advice
>>>>
>>>> Best wishes
>>>> Vlad
>>>>
>>>> --
>>>> Vlad Cojocaru, PD (Habil.), Ph.D.
>>>> -----------------------------------------------
>>>> Project Group Leader
>>>> Department of Cell and Developmental Biology
>>>> Max Planck Institute for Molecular Biomedicine
>>>> Röntgenstrasse 20, 48149 Münster, Germany
>>>> -----------------------------------------------
>>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>>> <http://mpi-muenster.mpg.de/>
>>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>>
>>>
>>
>
> --
> Vlad Cojocaru, PD (Habil.), Ph.D.
> -----------------------------------------------
> Project Group Leader
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> -----------------------------------------------
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru

-- 
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru

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