I have not followed the thread but concerning the solvation of a
protein using genbox you need to:
1- use a box of water that has the exact size of the final box you
want (you make it yourself using any tool you want) and you need to
define the box size of the protein file as the one of the water box
conformation. This is given on the last line of the gro file. Then
genbox -cp -cs should work fine.
2- you need to use a water box size larger than the one you need. This
solution is generally easier. You can generate a box using genconf -
nbox option. And again define the box size in the protein conformation
file and genbox will just do fine.
We generally use -vdwd 0.18. It is a good compromise for disturbing
the system the least.
Note that these uses have been discussed on the MARTINI forum several
times.
XAvier.
On Dec 11, 2012, at 9:05 AM, francesco oteri wrote:
Tanks to all for your advices,
I am going to check all the different aspect you suggested and I will
report the results as soon as possible.
Francesco
2012/12/11 Tsjerk Wassenaar <tsje...@gmail.com>
Hi,
Visualization is the key. If you check the structure right after
genbox,
you should be able to notice something odd. Apparently genbox has a
problem
with martini water, which probably means there is a problem with
monoatomic
solvents. The problem has been noted before, b ut I'm a bit too
lazy now to
check whether it was here or on the martini forum. Using a small
box with a
single water molecule for filling will solve the problem.
Cheers,
Tsjerk
On Tue, Dec 11, 2012 at 12:06 AM, Mark Abraham <mark.j.abra...@gmail.com
wrote:
On Mon, Dec 10, 2012 at 11:54 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 12/10/12 5:45 PM, francesco oteri wrote:
For Justin,
I need this water for one simple reason: less then 20nm doesn't
work....As
I said before
It seems you have identified the source of the problem, and it is
independent of box size. I questioned the box size because it
seemed
rather random and you had not shown any data for box sizes less
than 19
nm,
so I was curious how you arrived at the need for 20 nm, more than
double
the size of your solute.
It would be interesting to see if you could identify a minimum
box size
that does not require large numbers of solvent configurations to be
stacked
within the unit cell. The only reason I could see for what you're
reporting is if neighboring solvent blocks somehow get crossed to
produce
overlap when they should simply be next to one another. The
larger the
box, the greater the probability that this happens.
Yeah, that's probably it. The water box has many waters with x
coordinates
down at 0.000 and near 10.901, with an x size of 10.902. So
different box
sizes will randomly introduce unstable water configurations
according to
whether stuff is too close. This water box is probably not suited
to the
purpose - its "box size" might not include the half VDW radii
outside the
water coordinates needed to pack stably.
Mark
2012/12/10 francesco oteri <francesco.ot...@gmail.com>
Hi Mark,
you are right respect the -vdwd 0.4: In MARTINI tutorials they
suggest
to
use 0.21. Since I still got errors with this procedure, I
decided to
remove
water manually through vmd.
Looking carefully at the configurations, I found that the water
molecule
originating the error is exactly superimposed to an other
molecule
so I
simply deleted it and the same error is reported for an other
water
molecule.
Although I could scan all the pdb to detect all the superimposed
water
molecules, I believed genbox checked for this. Of course the
original
box
does't contain superimposed molecules.
It is highly unusual for genbox to produce overlapping waters,
but per
the
help description, only solute-solvent overlaps are checked, not
solvent-solvent, which would likely require enormous amounts of
memory
(and
genbox already has memory issues).
-Justin
--
==============================**==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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Cordiali saluti, Dr.Oteri Francesco
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