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. 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. If, however, I remove
the distance restraints, the simulation has no problem. 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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