[gmx-users] Advice for simulating small DNA

[Mark Abraham]

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: jballanc at gmail.com
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