Hi,
Thanks for the full description. It seems like your file system cannot
handle files over 2gb even for splitting, which is not surprising, because
the limitation is based on the use of a 32-bit integer. You should get
access to a better file system, where maybe your file can be read. You may
Hello:
I've got a question on the membrane protein simulation in Gromacs.
I noticed that both water and ions can wrap between up leaflet and low
leaflet. I am just wondering can we restrain both water and ions in the
same leaftlet? eg: the one in the up leaftlet always in the up leaftlet
during
Hi Albert,
Turn off PBC in the z-direction, or introduce a vacuum layer and set the
compressibility in the z-direction to zero.
Cheers,
Tsjerk
On Sun, Jan 26, 2014 at 9:29 AM, Albert mailmd2...@gmail.com wrote:
Hello:
I've got a question on the membrane protein simulation in Gromacs.
I
hi GMX users
The output of pdb2gmx told me that the protein-ligand complex has a net charge
of 0(zero)
but at the last line of my[ atoms ] directive in topol.top;qtot 2.749e-06 .
be read .
1)What does this mean?
2) if my system has a net charge of 0(zero),must iadd ions to my system for
On Jan 26, 2014 10:57 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com
wrote:
hi GMX users
The output of pdb2gmx told me that the protein-ligand complex has a net
charge of 0(zero)
but at the last line of my[ atoms ] directive in topol.top;qtot
2.749e-06 . be read .
1)What does this mean?
On 1/26/14, 3:07 AM, Mahboobeh Eslami wrote:
hi GMX users
i simulate protein ligand complex in dodecahedron box
when i use following command
editconf -f complex.pdb -o newbox.gro -bt dodecahedron -d 1.0 -c
My complex is not located in the center of box,
How do I put the complex in the
On Jan 26, 2014 9:30 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com
wrote:
hi GMX users
i simulate protein ligand complex in dodecahedron box
when i use following command
editconf -f complex.pdb -o newbox.gro -bt dodecahedron -d 1.0 -c
My complex is not located in the center of box,
How
Oh, what a wonderful PBC confusion :)
Actually, it is in the center of the triclinic cell corresponding to a
rhombic dodecahedron, but it is not in the center of the rectangular brick
representation of that, which is the default output representation. The
rhombic dodechahedron does not have an
After looking at the parameters used for Asp and Glu, I have found that those
are the ones I identified to use for my simulations of carboxylates.
However, there is no terminal methyl group on Asp or Glu, like there is on a
linear carboxylate. So, do you think it would be acceptable to use a
On 1/26/14, 2:50 PM, rankinb wrote:
After looking at the parameters used for Asp and Glu, I have found that those
are the ones I identified to use for my simulations of carboxylates.
However, there is no terminal methyl group on Asp or Glu, like there is on a
linear carboxylate. So, do you
10 matches
Mail list logo
