From: Laurent Chaloin (laurent.chaloin_at_cpbs.cnrs.fr)
Date: Sat Feb 13 2016 - 01:53:46 CST
I already saw one little mistake in the atom selection (group1),
"atom*N*umbers" and not atom*n*umbers (N in uppercase)
Le 13/02/2016 08:07, Abhishek TYAGI a écrit :
> 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
> 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
> Abhishek Tyagi
> PhD Student
> Chemical and Biomolecular Engineering
> Hong Kong University of Science and Technology
> Clear Water Bay, Hong Kong
-- ___________________________________________________________________________ Dr. Laurent CHALOIN Enzymes bactériennes de résistance aux antibiotiques de type aminoglycoside CNRS - FRE3689 Centre d’études d’agents Pathogènes et Biotechnologie pour la Santé (CPBS) 1919 Route de Mende 34293 MONTPELLIER Cedex 5 Tel: 33 (0)4 34 35 94 65 Fax: 33 (0)4 34 35 94 11
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