From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Aug 05 2014 - 03:15:46 CDT
Hi Charlie,
Depending on the length of the strands, the distance coordinates that you
are using could be insufficient to describe the process, especially if
there is a lot of twisting involved as well.
A while ago there was one ABF study on a related question:
http://pubs.acs.org/doi/abs/10.1021/jp0762323
That was a very local calculation, which is probably the reason why it went
well.
In the end you might have to decompose the process into several steps or
subprocesses described by different coordinates. They might happen
sequentially or concurrently.
Best,
Jerome
On 5 August 2014 08:54, 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
>
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