AMBER Archive (2009)

Subject: Re: [AMBER] Problem with RNA hairpin unwinding in explicit water

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Wed Apr 22 2009 - 18:10:55 CDT

Thank you, Thomas.
I'll work your suggestions into the simulation, and see what happens.

Sasha

Thomas Cheatham III wrote:
>> I'm trying to simulate a hairpin structure of RNA using an NMR structure
>> as a starting point (1MFY in PDB). However, the RNA unwinds from a
>> helical structure into a linear base-paired one. This happens within
>> several ns of simulation.
>>
>
> Anything this drastic happening so fast is a little suspect; normally we
> can simulate hairpin loop geometries with ff99 or ff99-bsc0 for 5-10's of
> ns without significant change. 50-100 ns is another story.
>
> - If you are restarting frequently, it could be the random seed problem
> with Langevin (see paper by Cerrutti/Duke and discussions in archives).
>
> - I do not think no salt would cause structure disruption and certainly
> not on this time scale as Ewald implicitly includes an effective salt
> (i.e. the net-neutralizing plasma). Years ago we looked at this in short
> simulations and saw little salt effect. However, perhaps as the defaults
> now get rid of excess charge, the problem could be related to
> net-neutralization of the overall large negative charge (thereby changing
> each of the charges). You would see this at the top of the mdout file,
> i.e. removing net-charge of X. But, if you have a lots of atoms, the
> change in charge is only +31/#atoms which is likely small. You could try
> to turn on the Ewald plasma (i.e. don't neutralize) but better would be to
> include a finite salt concentration. Somehow I do not think this is the
> origin of the problem.
>
> - If you see sugars systematically in the plane of the base (alternating)
> this is indicative of the alpha/gamma problem that ff99-bsc0 intends to
> overcome.
>
> - Note that with Ewald a cutoff of 15 is serious overkill and will cost
> your dearly in simulation time. I would recommend 8-9 angstroms with a 1A
> skin and the uniform van der Waals density correction (which is on by
> default).
>
> - Check to make sure your structure post-equilibration is OK.
>
> - You can probably get away with DT=0.002 (set the SHAKE tolerance
> tighter, i.e. smaller).
>
> --tec3
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber