Hi Justin,
Thanks again for the tip. I'm always assuming that there's something wrong
with my setup but I tested using one rank only and then I get an order of
magnitude smaller fluctuations... #underInvestigation
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Viveca
On Mon, Mar 12, 2018 at 6:42 PM, Justin Lemkul wrote:
>
>
> On 3/12/1
Hi Gregory,
It's periodically connected and I am applying adaptive biasing/pulling
(forgot to say). If you have special experience with that kind of setup,
I'd be interested in hearing it. Otherwise, it's quite standard, and yes,
parmbsc1.
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Viveca
On Mon, Mar 12, 2018 at 6:53 PM, Gregory Poon
On 3/12/18 1:40 PM, Viveca Lindahl wrote:
Hi Justin,
I'm using semi-isotropic pressure coupling and the periodicity is along z. I
should say that I'm also adaptively biasing a base pair to open, which is
triggering the fluctuations.
I guess you mean using only OpenMP? I have not tried that no
Hi Justin,
I'm using semi-isotropic pressure coupling and the periodicity is along z. I
should say that I'm also adaptively biasing a base pair to open, which is
triggering the fluctuations.
I guess you mean using only OpenMP? I have not tried that no, thanks for
the suggestion. Now I changed to
Hi Viveca,
Could you share more details of your simulations that may shed any
light? I assume that you are using parmbsc1 as the DNA forcefield. Is
it an "unusual" system? We (and I am sure others) simulate DNA (±
ligand) quite a bit and would be as interested in understanding what is
goin
On 3/12/18 10:42 AM, Viveca Lindahl wrote:
Hi Gregory,
In the sense that I see it happening repeatedly yes :) But I can't
reproduce it very predictably.
After seeing that (for my small system) I get very large box vector
fluctuations using Parrinello-Rahman, my current assumption is that ther
Hi Gregory,
In the sense that I see it happening repeatedly yes :) But I can't
reproduce it very predictably.
After seeing that (for my small system) I get very large box vector
fluctuations using Parrinello-Rahman, my current assumption is that there
are some stability assumptions made by mdrun
Since there hasn't been any response to your question yet, may I ask: is
it reproducible?
Gregory
On 3/11/2018 7:30 AM, Viveca Lindahl wrote:
Hi,
I'm running a simulation of a periodic DNA molecule. After some time I get,
sometimes the following error message:
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A list of mis