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...
For PME I was using:
coulombtype = PME
rlist = 0.55
rcoulomb = 0.55
rvdw = 0.55
fourierspacing = 0.1375
I agree with Justin that these are very weird for normal usage.
Thanks for pointing that out. I'm relatively new with Gromacs, and
hastily reduced these values to fix the relatively small box my
system fits in. I doubled the short box dimension (triclinic; was --
> 2.0, 2.1, 1.1 now --> 2.0, 2.1, 2.0) and increased the radii to
the (as far as I can tell) more recommended values:
coulombtype = PME
rlist = 0.9
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
Well, that's more like it. Values for these parameters are actually
intrinsic to the forcefield parametrization process, and one should
vary them only with caution. This algorithmic constraint sets a
minimum size for the simulation, of course.
When using PBC, just fitting your system into a box doesn't address
the real issue. In a real solution this 3-mer would be close to
infinite dilution, which can't be modeled without a serious chunk of
solvent around it. This consideration dwarfs the algorithmic one I
refer to above.
Unfortunately, even with all of these changes, I'm still getting an
explosion (and my simulation is quite a bit slower).
Anyone can get quick random numbers - you don't even need a
simulation package :-P There's no substitute for background
literature reading, doing tutorials, and experimenting with
preparedness for failure. :-)
Agreed, and thank you for all the help. I've decided to get a bit
creative, and work around the whole short-DNA fragment issue all
together. The new approach will also reduce the number of simulations
I'm looking at doing from ~6000 to ~20, so I don't have to worry about
the larger boxes taking so much longer to simulate.
Again, thanks for everything!
- Josh_______________________________________________
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