From: Jiyong Park (jiyongpark.77_at_gmail.com)
Date: Tue Nov 15 2016 - 20:28:32 CST
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.
(https://docs.google.com/document/d/1nHgApu2GjmloXPombGsBsOmZoT-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.
(https://docs.google.com/document/d/19SniI3Syjatcl6rRjG4-oUvVKCN2zCGbA24jxyp-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.
(https://docs.google.com/document/d/1X3UsOjIcm1Eqb4AAKTRbznuqZUpTYGBd7tUvjWNS_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
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:37 CST