Just short comment to that.
Water model can indeed have an effect on NA simulations,
but is not easy to pinpoit the physical "origin"
of that.
We have noticed visible water model difference
in RNA simulations
Understanding RNA Flexibility Using Explicit Solvent Simulations: The
Ribosomal and Group I Intron Reverse Kink-Turn Motifs
Author(s): Sklenovsky Petr; Florova Petra; Banas Pavel; et al.
Source: JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 7 Issue: 9
Pages: 2963-2980 DOI: 10.1021/ct200204t Published: SEP 2011
We tested several ion condititions and two water models.
We are trying to get more data on that right now.
Although the effect of water model (in contrast to ions)
may seem to be at first sight counterintuitive, in fact,
considering the number of waters interacting with NA and
its anionic nature, some kind of "coupling" between
solute and solvent force fields is not so surprising.
But it all is empirical, as always with force fields,
there is not necessarily some clear "physics" behind that.
Best wishes, Jiri
On Mon, 21 Nov 2011, Bruno Rodrigues wrote:
> Date: Mon, 21 Nov 2011 15:32:40 -0200
> From: Bruno Rodrigues <bbrodrigues.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Stability of water force fields
>
> The Temperature is quite high: 400K, and I'm using parmbsc0 on Amber11 for
> a 10bp short sequence.
>
> However my question is: what makes TIP4P and TIP5P less stable than TIP3P???
>
> Because I achieved a very nice result on the denaturation process using
> TIP3P with 2fs, but with both other force fields the energy started to
> drift until gets higher and higher values and the system became unstable,
> interacting with the 1st image, and so on.... Then I switch to 1fs and it
> nicely melted as expected.
>
> I've read your paper (J. Phys. Chem. B 2008, 112, 6013-6024) and followed
> your instructions there about the water force fields. Do you think that
> there might exist some kind of internal vibration on DNA that is very
> sensitive to Coulomb forces? I have accurately calculated the water
> self-diffusion for the TIP5P up to 400K, in long NVE simulations after NpT
> equilibration and found that for TIP5P it has a higher value than for both
> TIP3P and TIP4P. Can it be related with the stability of the system?
>
> I guess these are questions that still deserve much attention and research
> on this field, and the answers might not exist yet.
>
> Thank you in advance.
>
> On Mon, Nov 21, 2011 at 3:04 PM, David A Case <case.biomaps.rutgers.edu>wrote:
>
>> On Mon, Nov 21, 2011, Bruno Rodrigues wrote:
>>>
>>> It has been suggested here by the specialists (I guess David Case) that
>> for
>>> TIP4P and TIP5P water ffs the time step for solvated biomolecules should
>> be
>>> decreased.
>>>
>>> I have observed that high temperature DNA simulations are not stable at
>> 2fs
>>> for these two ffs, obligating me to go down to 1.5 and 1.0fs
>> respectively.
>>
>> It's hard to say much here. We don't know what temperature you are using,
>> what DNA force field, or what the definition of "not stable" is.
>>
>> I might make two general comments. First, DNA is kind of on the "edge" of
>> stability with current force fields, and once some strands start to
>> unravel,
>> that process can continue. I'd guess that using high temperatures would
>> exacerbate this.
>>
>> Second, 2fs time steps are also pushing things. They almost always require
>> thermostatting to keep the temperature from drifting, and the extra energy
>> is often very localized (arising from a badly-integrated atomic collision),
>> which can sometimes disrupt local structure in a way that is not
>> re-annealed.
>> I generally use 1fs steps, but sometimes don't. Clearly, if you are seeing
>> problems at 2fs that seem to go away at 1fs, you should probably be using
>> the short time step.
>>
>> ....dac
>>
>>
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>
>
>
> --
> --
> Bruno Barbosa Rodrigues
> PhD Student - Physics Department
> Universidade Federal de Minas Gerais - UFMG
> Belo Horizonte - Brazil
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Received on Tue Nov 22 2011 - 06:00:03 PST
