From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat Feb 13 2016 - 13:21:00 CST
Both are acceptable methods of selecting atoms. Atomnumbers will let you
cherry pick the atoms, whereas atomNumbersRange will include all atoms
within a range.
However, in your colvar-1.conf there appears to be a missing brace.
On Feb 13, 2016 2:09 AM, "Abhishek TYAGI" <atyagiaa_at_connect.ust.hk> wrote:
> Dear Experts,
> 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:
> 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
> Abhishek Tyagi
> PhD Student
> Chemical and Biomolecular Engineering
> Hong Kong University of Science and Technology
> Clear Water Bay, Hong Kong
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