Potential of CG water with IBI : difference between published version and the one I obtain from VOTCA

[massimo sandal]

Hi,

To learn VOTCA, I am trying to reproduce the water potential as in the original VOTCA paper, using IBI (Ruhle et al.,  J. Chem. Theory Comput., Vol. 5, No. 12, 2009 , fig. 2A). Unfortunately it seems that I can't. The RDF converges very quickly and very well, but the potential is completely different from the one of the paper. This happens even with the tutorial files (v. 1.2.2)

See here for an example of what I mean: http://imgur.com/a/c74Yw

I am using Gromacs 4.5.5 single precision. The only difference in the settings file from the tutorial is where I specify the name of the binaries. The settings.xml is attached. The trajectories at each step seem healthy, visually.

What can I do to troubleshoot this?

Thanks,
Massimo

[Victor Ruehle]

Dear Massimo,

the potentials indeed looks a bit funny. I'm currently running the
tutorial to verify everything is correct in there. Will get back to
you later.

As a general remark, very different potentials can lead to almost
identical RDFs. When we did the simulations, the RDF looked great
after 5-10 iterations, but then it took another ~200 to get to its
final shape.

Victor

2012/9/25 massimo sandal <device...@gmail.com>:

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[massimo sandal]

the potentials indeed looks a bit funny. I'm currently running the
tutorial to verify everything is correct in there. Will get back to
you later.

Thanks!
 

As a general remark, very different potentials can lead to almost
identical RDFs. When we did the simulations, the RDF looked great
after 5-10 iterations, but then it took another ~200 to get to its
final shape.

I suspected that, yet previous tests I did (I was using my own water simulations instead of the tutorial, with basically identical results) showed that the final shape is indeed the same. I am still running the IBI tutorial, will report you as soon as it finishes. So far we are at step_125 and it still looks more of the same :)

I wonder how much potential discrepancies would affect AdResS simulations (that are my final aim).

Thanks,
Massimo

[Victor Ruehle]

For me the tutorial seems to run smoothly so far. What worries me a
bit in your case is the magnitude of the CG-CG potential. Could you
please send your whole input folder where you run the simulation
(excluding the step_???) directly to rue...@votca.org ?

I cannot comment on Adress, but Christoph or Sebastian should know more.

Thanks,

Victor

2012/9/25 massimo sandal <device...@gmail.com>:
>

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[ms]

On 25/09/12 15:34, Victor Ruehle wrote:
> For me the tutorial seems to run smoothly so far. What worries me a
> bit in your case is the magnitude of the CG-CG potential.

It worried me too.

> Could you
> please send your whole input folder where you run the simulation
> (excluding the step_???) directly to rue...@votca.org ?

Sure, thanks!!
Massimo

--
Massimo Sandal, Ph.D.
http://devicerandom.org

[ms]

On 25/09/12 15:34, Victor Ruehle wrote:

> For me the tutorial seems to run smoothly so far. What worries me a
> bit in your case is the magnitude of the CG-CG potential. Could you
> please send your whole input folder where you run the simulation
> (excluding the step_???) directly to rue...@votca.org ?

Wait. I just suspect it was a dumb error on my part -namely, I was
probably plotting the derivatives (force)?

[Victor Ruehle]

Oh, yea. Looking at the row numbers you plotted that seems to be the case :)

you can also check the votca potential tables: CG-CG.pot.new / CG-CG.pot.cur

Victor

2012/9/25 ms <device...@gmail.com>:

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[ms]

On 25/09/12 17:46, Victor Ruehle wrote:
> Oh, yea. Looking at the row numbers you plotted that seems to be the case :)

Indeed I checked and the potential converges nicely. Sorry for wasting
your time. Dammit, it's a bit I don't use tables in Gromacs and my
memory was a bit rusty.

> you can also check the votca potential tables: CG-CG.pot.new / CG-CG.pot.cur

Right, thanks.

Sorry again and thanks,
Massimo

[Victor Ruehle]

Hehe, np. good that this was sorted out so easily.