Re: Metadynamics simulation

From: Azadeh Alavi (azade.alavi_at_gmail.com)
Date: Thu Jan 05 2017 - 06:39:34 CST

Hello Giacomo

Thanks a lot for your explanations. I upgraded to NAMD2.12 and the problem
was solved,and as your said, the performance also improved.

One more question is that is it possible to do bias-exchange metadynamics
with NAMD and Plumed or one should turn to GROMACS?

Thank you very much for your time and help.

Best,
Azadeh

On Wed, Jan 4, 2017 at 9:46 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213 <(215)%20204-4213>
>
> Scholar: http://goo.gl/Q3TBQU
> Personal: http://giacomofiorin.github.io/
> Lab page: https://icms.cst.temple.edu/members.html
>
> *"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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