RE: Regarding colvar distancez

From: Cosseddu, Salvatore (
Date: Sat Mar 08 2014 - 07:44:39 CST

Dear Subbarao,

In the first case one of your processor is computing the center of mass of 30207 atoms every time step... slowing down all the computation.

>From the manual:
Performance issues: While NAMD spreads the calculation of most interaction terms over many computational nodes, the colvars calculation is not parallelized. This has two consequences: additional load on the master node, where the colvar calculation is performed, and additional communication between nodes. NAMD's latency-tolerant design and dynamic load balancing alleviate these factors; still, under some circumstances, significant performance impact may be observed, especially in the form of poor parallel scaling. To mitigate this, as a general guideline, the size of atom groups involved in colvar components should be kept small unless necessary to capture the relevant degrees of freedom.

Solutions are two:

1. Smaller reference;

2. Wait... and select the number of cores depending on this choice (you don't need 30000 cores if everything is slowed down by the COM calculations on one of them)

In the dummy atom case, you are selecting just one group and a position. Which is the second group you are referring to?




From: <> on behalf of Subbarao Kanchi <>
Sent: 08 March 2014 11:00
Subject: namd-l: Regarding colvar distancez

Dear all,
            I am using the fallowing colvar (distancez) to do umbrella sampling.I used ref { atomNumbersRange 1-30208} to define reference group,It makes simulation very slow (~1ns/4days) but If I use ref { dummyAtom (0.0, 0.0, 0.0)} simulation is as fast as normal MD (~4ns/day). If I used the dummy atom, the actual distance between center of masses between two groups are not maintaining. I checked mailing list but I did not find any discussion on this problem. I will appreciate any suggestions in this regard.

Subbarao Kanchi.

colvarsTrajFrequency 1000
colvarsRestartFrequency 1000

colvar {

        width 0.5
        name lipid
        distancez {
                   main { atomNumbersRange 30209-31494}
                   ref { atomNumbersRange 1-30208}
                   axis (0.0, 0.0, 1.0)

harmonic {
          colvars lipid
          centers 57.97
          forceConstant 500.0
          targetCenters 60.0
          targetNumSteps 1000000

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