Joshua Ballanco wrote:
On Feb 1, 2009, at 6:48 PM, Mark Abraham wrote:
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!)
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
get it?
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.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
