[gmx-users] Advice for simulating small DNA
Mark.Abraham at anu.edu.au
Mon Feb 2 02:22:10 CET 2009
Joshua Ballanco wrote:
> On Feb 1, 2009, at 6:48 PM, Mark Abraham wrote:
>> 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!)
> Apologies for not being more descriptive... It is a single strand of DNA
> containing 3 A-T base pairs. The system also contains a single Arginine
> residue. Simulating it in water leads to the single DNA strand gradually
> coming apart. With the DNA and water alone, the helix stays together
> much longer, but still eventually comes apart.
OK, so your model physics for DNA is intrinsically broken. Where did you
>>> 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.
> As I understand, the only relevant lines are:
> constraints = all-bonds
> integrator = md
> disre = simple
disre-fc and others are also relevant. See manual chapter 7.
> For PME I was using:
> coulombtype = PME
> rlist = 0.55
> rcoulomb = 0.55
> rvdw = 0.55
> fourierspacing = 0.1375
I agree with Justin that these are very weird for normal usage.
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