Re: restarting Gaussian accelerated MD fails

From: Miao, Yinglong (miao_at_ku.edu)
Date: Fri Aug 03 2018 - 16:58:34 CDT

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

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


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