From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Jun 13 2017 - 12:09:32 CDT
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:
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:
-Josh
On 06/09/2017 11:35 AM, The Cromicus Productions wrote:
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_at_gmail.com>>> wrote:
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_at_gmail.com>>> wrote:
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_at_gmail.com>>> wrote:
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:
Adding a "patch" to your topology file is the easiest way.
The key here is the patch command. My "PBCrna" patch, in the topology file, looks like:
That's it!! The "regenerate" command generates the correct bends and dihedrals to
Note: in VMD the bond will be drawn across the box, but that is just how VMD displays
-Steve
________________________________________
Hi everyone,
I'd like to simulate an infinitely long, periodic dsDNA in NAMD.
Thank you very much,
Sebastian
This archive was generated by hypermail 2.1.6
: Sun Dec 31 2017 - 23:21:22 CST
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
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.
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?
I found the problem, it's not the same to add res 1 70 than 70 1 hehe
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?
Thank you very much, Steve! I used the patch "LKNA" instead of "PBCrna" and I think it worked great!
Hi Sebastian,
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
-----------------------------------
-------------
PRES PBCrna 0.0
BOND 1P 2O3'
--------------
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.
it, it really it across the PBC.
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
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?