From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Sat Feb 13 2016 - 01:07:38 CST
I am using replica exchange umbrella sampling. My aim is to calculate the PMF using REUS, therefore, I am using distance variable to understand the movement between the two molecules. I have two molecules molecule 1 and molecule 2, the molecule 1 is protein and molecule 2 is nano particle. I had selected all CA from molecule 1. I am following the tutorial available in NAMD(Method of calculating PMF and ) to execute the REUS. My colvar file is attached, I was using colvars.conf initially and now want to use colvar-1.conf, I would like to ask suggestion for the colvar "distance", in first file I have selected two groups as atomnumbers and atomNumbersRange to select the molecules. Is it correct or I need to use the colvar-1.conf format group1 atomnumbers and group2 atomnumbers.
While running the simulations, the first file I had run was running successfully, although the colvar-1.conf responded the following error:
Charmrun> scalable start enabled.
Charmrun> started all node programs in 0.110 seconds.
Charm++> Running in non-SMP mode: numPes 16
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Charm++> TORUS A SIZE 16 USING 0 1 2 3 4 5 6 7 8 9...
Charm++> TORUS B SIZE 1 USING 0
Charm++> TORUS C SIZE 1 USING 0
Charm++> TORUS MINIMAL MESH SIZE IS 16 BY 1 BY 1
Redirecting stdout to files output/0/job2.0.log through 15
------- Partition 8 Processor 0 Exiting: Called CmiAbort ------
Reason: REPLICA 8 FATAL ERROR: Error in the collective variables module: exiting.
Fatal error on Partition 8 PE 0> REPLICA 8 FATAL ERROR: Error in the collective variables module: exiting.
Any help is will be very helpful.
Thanks in advance
Chemical and Biomolecular Engineering
Hong Kong University of Science and Technology
Clear Water Bay, Hong Kong
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:48 CST