The biotin-streptavidin interaction is on the order of -75 kJ/mol, so a binding
free energy of -300 kJ/mol (dissociation constant of 10^-52 M) means something
is fundamentally wrong - start by taking a hard look at your protocol, as
convergence problems wouldn't account for that kind of deviatio
Dear Justin,
Firstly, Thanks for your help. You said "You're going from the end of chain
B to the beginning of chain A, then back to B later on. Also realize that
whatever "ABSG" or "BSG" is." How do you understand it? Where can I find
such an important theoretical information?
Thanks in advance
On 30/12/2010 11:37 PM, ahmet yıldırım wrote:
Dear Justin,
Firstly, Thanks for your help. You said "You're going from the end of
chain B to the beginning of chain A, then back to B later on. Also
realize that whatever "ABSG" or "BSG" is." How do you understand it?
Where can I find such an im
Hi Solomon,
Just stumbled upon your mail and I thought you could still use a
answer to your question.
First of all, as you've probably read on the Gromacs-GPU page, a) you
need a high-performance GPU to achieve good performance (in comparison
to the CPU) -- that's the reason for the strict compat
Hi,
I've never seen/had my hands on the Tesla T10 so I didn't know that's
the name it reports. I'll fix this for the next release. Rest assured
that on this hardware Gromacs-GPU should run just fine.
On the other hand, your driver version is very strange: CUDA Driver
Version = 4243455, while it s
Dear gromacs users
My simulation system contains protein, dna, water molecules and Na+
ions respectively.
I want to reorder water molecules with Na+ ions in final xtc file as
at first
1-1867 complex (protein and dna)
1868 - 24085 SOL (water molecules)
24086 -
Dear Leila:
Perhaps I took the long way around, but I am not aware of any such
tool. You can make custom modifications to things like trjconv as
follows.
!!! Please note: I didn't test this except to see that it compiles.
You should run some analyses before and after switching the order t
Thank you Chris for your answer:
1) The molecule has no net charge because the virtual site in the center
of mass is a point charge twice the charge in the O atom.
2) Until now I've created 5 files but I don't know if I am doing the
right thing:
* forcefield.itp
#define _FF_OXY
[ defau
Hi!
We figured we'd celebrate the upcoming new year with some major changes in the
git development branch, consisting primarily of C++ support and a more modular
organization of files.
This is a gradual process, so this mail is a bit of a warning-message that the
master/development branch might
Hi!
We figured we'd celebrate the upcoming new year with some major changes in the
git development branch, consisting primarily of C++ support and a more modular
organization of files.
This is a gradual process, so this mail is a bit of a warning-message that the
master/development branch might
Sorry Marcelo, that sounds like a job for an author ;) If nobody else
chimes in, then I suggest that you do some testing and come back to
the list with specific problems. As an analogy, you might look at how
the virtual site is handled in tip4p in the absence of settle.
Chris.
-- original
Dear GMXers,
I'm simulating a SPC/E water box with the size of 4nm by 4nm by 4nm. The
command "g_tune_pme" was used to find the optimal PME node numbers, Coulomb
cutoff radius and grid spacing size.
The following command is used:
g_tune_pme -np 24 -steps 5000 -resetstep 500 ...
rcoul=1.5nm, rvdw=
On 31/12/2010 5:03 AM, Marcelo Silva wrote:
Thank you Chris for your answer:
1) The molecule has no net charge because the virtual site in the
center of mass is a point charge twice the charge in the O atom.
2) Until now I've created 5 files but I don't know if I am doing the
right thing:
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