Holes... Holes... What is the size of these holes? Use g_density,
g_rdf, make plots, observe peaks...
> Hi Diana,
>
> Yeah, my reply was a bit off, as Vitaly had already pointed out. Lazy
> reading, sorry. But are these holes created by genbox, or are they already
> present in the acn solven box
Hi Diana,
Does it also happen if you solvate the box without the protein? And are the
holes close to the protein or just anywhere? And what makes it difficult to
analyze the structure output by genbox directly, perhaps specifying that the
output be .pdb? It's what I usually do.
Cheers,
Tsjerk
O
Hi,
It seems to me that the holes are created by genbox because I don't have
them in the original solvent box. The intermediate box (outputed by trjconv)
with the protein solvated but not converted is difficult to analyze, because
the box doesn't have the right shape and of pbc issues, but it seem
Hi Diana,
Yeah, my reply was a bit off, as Vitaly had already pointed out. Lazy
reading, sorry. But are these holes created by genbox, or are they already
present in the acn solven box? Have you already checked all intermediate
structures?
Cheers,
Tsjerk
On Nov 6, 2010 7:25 PM, "Diana Lousa" w
Hello,
No, the hole don't correspond to parts of the protein sticking out on the
other side. The protein is in the center of the box and the holes are not
due to pbc issues.
Diana
On Fri, Nov 5, 2010 at 10:10 PM, Tsjerk Wassenaar wrote:
> Hey,
>
> Do the holes match the parts of the protein s
She uses "trjconv -pbc atom", so it looks like the answer is no.
On Fri, Nov 5, 2010 at 6:10 PM, Tsjerk Wassenaar wrote:
> Hey,
>
> Do the holes match the parts of the protein sticking out on the other side?
>
> Tsjerk
>
>
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Hey,
Do the holes match the parts of the protein sticking out on the other side?
Tsjerk
On Nov 5, 2010 8:14 PM, "Vitaly Chaban" wrote:
On Fri, Nov 5, 2010 at 3:03 PM, vedat durmaz wrote:
> hi vitaly,
>
> the only acetonitrile boxe that i was able to find is the one provided by
> christoph fre
On Fri, Nov 5, 2010 at 3:03 PM, vedat durmaz wrote:
> hi vitaly,
>
> the only acetonitrile boxe that i was able to find is the one provided by
> christoph freudenberger in 2003:
>
> http://www.gromacs.org/@api/deki/files/34/=mecn_box.tgz
Maybe somewhere on other old website if they lost it while
Diana -
I just wonder how the density of your system behaves while you run NPT
equilibration? Do you monitor it? Did you estimate the size of these
holes? Maybe they are just due to a visualization utility that uses
inappropriate atomic radii?
Vitaly
On Fri, Nov 5, 2010 at 2:05 PM, dlousa wro
Hey, Diana -
I believe these acetonitrile holes are not a problem. Just perform an
equilibration run in the NPT ensemble and they will disappear. The
more tricky way is to adjust VDW radii in vdwradii.dat before using
genbox.
By the way, what force field model of acetonitrile do you use here?
Som
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