[gmx-users] Advice for simulating small DNA

[Joshua Ballanco]

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: jballanc at gmail.com