Re: [NAMD] How to build and simulate a periodic DNA in NAMD

From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Sun Jun 18 2017 - 17:47:39 CDT

Thanks for your reply, Josh! Actually that was not the problem, as I am
working with dsDNA and the base stacking forces are large enough. The
problem is that I was considering the flexible cell during minimization and
heating, once I only considered it during equilibration that worked like a
charm.
Regards,

Sebastian

On Tue, Jun 13, 2017 at 1:09 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Is this meant to be one long stretch of RNA? I don't see bonds that span
> the periodic box, which means they aren't connected together like I thought
> you were aiming for. Right now, the box is expanding along that axis since
> the negative charges associated with RNA ends are pushing the system apart,
> and there is no covalent bond to hold them together.
>
> -Josh
>
> On 06/13/2017 04:42 AM, The Cromicus Productions wrote:
> 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.
> protection.outlook.com/?url=https%3A%2F%2Fstreamable.com%
> 2Frqpp0&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%
> 7C275907d0905544e89e5408d4b248d356%7Ca0f29d7e28cd4f5484427885aee7
> c080%7C1%7C0%7C636329473243899028&sdata=Omhl3WnGOWlMVC24fo7Nc0CX9v7E02
> wxpdWnUdXD%2FCM%3D&reserved=0>
>
> Any suggestion?
>
>
> On Fri, Jun 9, 2017 at 1:42 PM, Vermaas, Joshua <
Joshua.Vermaas_at_nrel.gov<
> mailto: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
> ><mailto:thecromicusproductions_at_gmail.com<mailto:thecromicusproductions@
> 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
> ><mailto:thecromicusproductions_at_gmail.com<mailto:thecromicusproductions@
> 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
> ><mailto:thecromicusproductions_at_gmail.com<mailto:thecromicusproductions@
> 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><mailto:
> 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><mailto:
> 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><mailto:
> 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><mailto: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
>
>
>
>
>
>
>
>
>

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