Joshua Ballanco wrote:
On Feb 2, 2009, at 12:26 AM, Mark Abraham wrote:
No, I've no idea since I don't simulate DNA.
In that case, thank you the help that much more!
So I'm now attempting to add restraints for the base-pair
H-bonds, but I'm having trouble. It seems like no matter what I
try, my system reliably explodes within the first 1 ns. My
constraints look like this:
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
18 136 1 0 2 0.0 2.0 2.1 1.0
14 134 1 0 2 0.0 2.0 2.1 1.0
43 114 1 0 2 0.0 2.0 2.1 1.0
39 112 1 0 2 0.0 2.0 2.1 1.0
68 92 1 0 2 0.0 2.0 2.1 1.0
64 90 1 0 2 0.0 2.0 2.1 1.0
I've tried pre-equilibrating for up to 100 ps, but even that
doesn't prevent the system from eventually exploding.
Your .mdp settings for distance restraints may also be relevant
here - not least in setting the existence and magnitude of these
restraints.
As I understand, the only relevant lines are:
constraints = all-bonds
integrator = md
disre = simple
disre-fc and others are also relevant. See manual chapter 7.
Thanks for the pointer. I had overlooked most of the options there,
since I'm not actually doing anything related to NMR. (That'll teach
me to read more carefully!) Unfortunately, playing around with this,
disre-tau, disre-weighting, and the weighting factors for each bond
have not, so far, avoided the explosion.
OK, that's no longer surprising - distance restraints will not
usefully fix a broken model physics.
Well, yes, but I also wouldn't expect them to break the broken physics
further... I realize the system I was using originally was rather
unphysical, but the DNA helix at least was at least *mostly* holding
together. When I add the distance restraints, even with very large
multipliers, the seem to serve only to tear apart the helix. Odd...
Shrug. Resonance can do weird things - just ask the Tacoma Narrows bridge!
Mark
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