Re: restarting Gaussian accelerated MD fails

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Wed Aug 08 2018 - 11:35:44 CDT

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, http://www.ks.uiuc.edu/~dhardy/
> On Aug 3, 2018, at 4:58 PM, Miao, Yinglong <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 <http://www.mpi-muenster.mpg.de/43241/cojocaru>
>> 
> 

This archive was generated by hypermail 2.1.6 : Sun Sep 15 2019 - 23:19:56 CDT