Re: Crashes with dihedral PC

From: Giacomo Fiorin (
Date: Tue Nov 15 2016 - 22:40:17 CST

Hello Jiyong, this is a significant jump in version numbers, but you
should be able to continue such simulation nonetheless.

Can you post or send off-list the links to download the configuration files
(NAMD and Colvars both) and the state/restart files necessary to test the


On Tue, Nov 15, 2016 at 9:28 PM, Jiyong Park <>

> Dear NAMD developers,
> Hello. I've been using dihedral PC (dPC)+metadynamics algorithm
> in NAMD v2.9 and decided to migrate toward the latest version.
> While testing v2.12, I recognize my simulation crashes
> at the first step of energy calculations.
> Attached links please find the top portions of the output messages
> generated.
> (
> mZoT-wV2zbtv5BRncmbwA/edit)
> NAMD_2.12b2.out.w_dPC shows the output message from
> v2.12b2 that is compiled with mvapich2+icc+cuda. I also tested the
> precompiled executables provided by the NAMD website, that
> resulted the same error messages.
> (
> vVKCN2zCGbA24jxyp-zUo/edit)
> NAMD_2.9.out.w_dPC shows the output messages from v2.9.
> The simulation went through for 75k steps without any problem.
> (
> uqZUpTYGBd7tUvjWNS_bo/edit)
> NAMD_2.12b2.out.wo_dPC shows the output message without
> the dihedral PC colvar. In this case, the simulation worked well
> for 75k steps.
> All the best,
> Jiyong

Giacomo Fiorin
Associate Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213
Lab page:
*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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