From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Tue Jun 13 2017 - 05:42:00 CDT
Thanks for your reply, Joshua. I tried that and I'm not sure of why but my
main DNA is stretching (as expected) but the ones at the left and right are
also stretching but moving farther away from the central one. In the
following link there's a video of what's going on:
https://streamable.com/rqpp0
Any suggestion?
On Fri, Jun 9, 2017 at 1:42 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:
> Hi Sebastian,
> This sounds similar to the issues faced with periodic cellulose
> simulation. For cellulose, what you typically do is equilibrate at constant
> pressure for a little bit, but allow the motion of the periodic cell to
> differ along the cellulose axis and the non-cellulose axis. In NAMD
> parlance, this would require setting useFlexibibleCell and
> useConstantRatio. The initial z-axis dimension would be the length of your
> DNA (at least what you think it ought to be), and the x and y dimensions
> are set so you have enough of a water buffer. During equilibration, the DNA
> should sort itself out, assuming the helix is close to repeating at the
> length you are interested in.
>
> -Josh
>
> On 06/09/2017 11:35 AM, The Cromicus Productions wrote:
> Hi everyone, sorry to come back to this but there's something I haven't
> been able to solve and that is
> how to work with the boundary conditions of the box. I would guess in
> order to simulate the periodic DNA
> the first and last nucleotides must be very close and we shouldn't have
> any water in the middle. Also, the distances
> involved should be the same than for a regular pair of base pairs. How can
> this be solved? Do I just consider
> a slightly smaller box than my DNA and hope for the best during
> minimization?
>
> Thanks!
>
> Sebastian
>
> On Sun, May 7, 2017 at 1:03 AM, The Cromicus Productions <
> thecromicusproductions_at_gmail.com<mailto:thecromicusproductions_at_gmail.com>>
> wrote:
> I found the problem, it's not the same to add res 1 70 than 70 1 hehe
>
> On Sun, May 7, 2017 at 12:30 AM, The Cromicus Productions <
> thecromicusproductions_at_gmail.com<mailto:thecromicusproductions_at_gmail.com>>
> wrote:
> Sorry to bother again, I'm currently running into a problem of the kind
> "UNABLE TO FIND ANGLE PARAMETERS FOR..." the atoms that I have
> just bonded. Have you ran into that problem before?
>
> On Sat, May 6, 2017 at 8:02 PM, The Cromicus Productions <
> thecromicusproductions_at_gmail.com<mailto:thecromicusproductions_at_gmail.com>>
> wrote:
> Thank you very much, Steve! I used the patch "LKNA" instead of "PBCrna"
> and I think it worked great!
>
> On Sat, May 6, 2017 at 2:49 PM, Nielsen, Steven <
> steven.nielsen_at_utdallas.edu<mailto:steven.nielsen_at_utdallas.edu>> wrote:
> Hi Sebastian,
>
> Adding a "patch" to your topology file is the easiest way.
> In my case, which is for the helical RNA strand in the TMV virus,
> I wanted to make the RNA strand infinitely long.
> My "pgn" file looks like:
> ---------------------------------
> package require psfgen
> topology top_all27_prot_na_SON.inp
> # add RNA
> segment RNA {first none; last none; pdb rna.pdb}
> coordpdb rna.pdb RNA
> patch PBCrna RNA:1 RNA:150
> guesscoord
> regenerate angles dihedrals
> guesscoord
> writepdb x.pdb
> writepsf x.psf
> -----------------------------------
>
> The key here is the patch command. My "PBCrna" patch, in the topology
> file, looks like:
> -------------
> PRES PBCrna 0.0
> BOND 1P 2O3'
> --------------
>
> That's it!! The "regenerate" command generates the correct bends and
> dihedrals to
> accompany the bond that I added. This patch adds a bond between atom "1P"
> on the
> first RNA base and the atom "2O3'" on the last (#150) RNA base.
>
> Note: in VMD the bond will be drawn across the box, but that is just how
> VMD displays
> it, it really it across the PBC.
>
> -Steve
>
>
> ________________________________________
> From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> [
> owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>] on behalf of
> The Cromicus Productions [thecromicusproductions_at_gmail.com<mailto:
> thecromicusproductions_at_gmail.com>]
> Sent: Saturday, May 6, 2017 1:14 PM
> To: NAMD list
> Subject: namd-l: [NAMD] How to build and simulate a periodic DNA in NAMD
>
> Hi everyone,
>
> I'd like to simulate an infinitely long, periodic dsDNA in NAMD.
> To do so I read in Nano Lett., 2015, 15 (12), pp 8322-8330 that I must
> covalently bond the ends of the DNA to their periodic copies.
> Any idea of which would be the easiest way to do this?
>
> Thank you very much,
>
> Sebastian
>
>
>
>
>
>
>
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:22 CST