Re: Metadynamics simulation

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jan 04 2017 - 12:16:25 CST

Hello Azadeh

On Tue, Jan 3, 2017 at 10:00 AM, Azadeh Alavi <azade.alavi_at_gmail.com> wrote:

> Dear NAMD users,
>
> I am going to perform Metadynamics simulations for ion transport through a
> protein. I am using NAMD2.11. I have copied the input file below.
> First, I was wondering if a timestep of 2 fs is OK to run this simulation
> and whether the parameters below are reasonable.
>

To have any chance of giving meaningful results, the metadynamics forces
should be much smaller than the ones generated from the force field, so the
same criteria of the unbiased simulation would apply for the time step.

> Secondly, when I run this simulation, the output file of HillsTrajectory
> is empty which is weird.
>

This a glitch caused by a redesign of the file i/o interface for NAMD prior
to the release of NAMD 2.11. The hills are being added, and you should be
able to see them in the state file. Also, you should notice an applied
force in the colvars trajectory.

Please upgrade to NAMD 2.12. You should also gain performance improvements
because certain variables such as distanceZ are now computed fully in
parallel.

Giacomo

>
> Thanks a lot for your help.
> Azadeh
>
>
>
> colvar {
> name Translocation
> lowerBoundary -4.0
> lowerWallConstant 100.0
> upperBoundary 56.0
> upperWallConstant 100.0
> width 0.4
> outputVelocity on
> outputAppliedForce on
>
> distanceZ {
> main {
> atomnumbers { 131678 }
> }
> ref {
> atomnumbers { protein alpha carbons..
> }
> }
> axis ( 0.0, 0.0, 1.0 )
> }
> }
>
> metadynamics {
>
> colvars Translocation
> hillWeight 0.01 # Default is 0.01 - higher numbers = faster
> newHillFrequency 100 # Default is 100 - lower numbers = faster
> writeFreeEnergyFile on
> saveFreeEnergyFile on
> keephills on
> writeHillsTrajectory on
> }
>

-- 
Giacomo Fiorin
Associate Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
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*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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