[gmx-users] Advice for simulating small DNA
Mark.Abraham at anu.edu.au
Mon Feb 2 00:48:01 CET 2009
Joshua Ballanco wrote:
> 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.
> 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!
> Joshua Ballanco
> Graduate Student
> Department of Chemistry and Chemical Biology
> Stevens Institute of Technology
> Hoboken, NJ 07030
> E-mail: jballanc at gmail.com
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users