VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Aug 04 2014 - 20:35:35 CDT

charlie,

your chances to get help will be significantly improved, if you post
to the proper mailing list, i.e. the one covering NAMD and not the one
on VMD.

axel.

On Mon, Aug 4, 2014 at 8:40 PM, Charles Whidborne
<charles.whidborne_at_student.adelaide.edu.au> wrote:
> Hi,
>
> I am running simulations on DNA in which i have equilibrated it over so many
> nanoseconds and now i want to measure the free energy of separating the
> strands using adaptive biasing force (ABF) in NAMD, but due to my
> inexperience (and probably lack of understanding) i am having trouble
> running the simulation successfully. I have done the ABF tutorials but they
> dont seem to help much when I try to relate it to my problem.
>
> In my NAMD config file i have:
> colvars on
> colvarsConfig Distance.in
>
> In my Distance.in file i have set:
> colvarsTrajFrequency 200
> colvarsRestartFrequency 2000
>
> colvar {
> name COMDistance
>
> width 0.1
> lowerboundary 1.0 -Not sure if these two boundaries are set
> appropriately.
> upperboundary 32.0
>
> distance {
> group1 {
> atomnumbers { #'s for back bone of one strand }
> }
> group2 {
> atomnumbers { #'s for backbone of second strand }
> }
> }
> }
>
>
> abf {
> colvars COMDistance
> fullSamples 500
> hideJacobian
> }
>
> I have had a couple simulations result in the partial separation of the
> strands, but as far as i can tell, due to the wrapping around each other the
> strand then gets 'stuck' trying to be pulled around the second strand...
> Any help or advice would be great on this.
>
> Thanks,
> Charlie 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.