Joshua Ballanco wrote:
Hi,
I'm attempting to model a system involving a small DNA 3-mer. Without
any explicit constraints, the helix begins to come apart around 0.75 ns
to 1 ns into the simulation.
Presumably you have a 3-mer of helices, of which at least one comes
apart. Does a single helix in water survive? (Giving a better
description of your simulation system would be a good idea!)
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.
If, however, I remove the
distance restraints, the simulation has no problem.
Hmmm? This seems to contradict what you say above.
Mark
I've also tried
instead of having distance_restraints, using a harmonic potential ([
bond ] with type=6), but I haven't been able to find any suggestions for
parameterizing the harmonic potentials. I played with a few values, but
even the harmonic potential is causing the system to explode.
I'm currently using the GROMOS96 53a6 force field with a triclinic box
(~2, ~2, ~1,2), PME with grid spacing 1.375, two component v-rescale
T-coupling, and no P-coupling. I'm using a 2 fs step, and I'd like to
avoid having to change any parameters that will have an impact on run
time (I'm less concerned about strict physical accuracy as I am with the
ability to run ~6000 of these simulations in a reasonable amount of time).
If anyone has any advice, I'd greatly appreciate it. Thanks!
Sincerely,
Joshua Ballanco
Graduate Student
Department of Chemistry and Chemical Biology
Stevens Institute of Technology
Hoboken, NJ 07030
E-mail: [email protected]
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