Is there any publication regarding this Fe-CO covalent bond breaking ?
Actually in experimental techniques, the bond between Fe-CO in myoglobin
gets broken in100 ps time scale. Is't possible to do this process by QM/MM
methods or ReaxFF? Please need an advice. I haven't have any
prior knowledge on
hi all,
I would like to measure the hydrophobic interaction of the ligand against
the protein during the simulation . From the forum I learnt g_mindist will
be the better tool. But when i used the command g_mindist -f traj.xtc -s
topol.tpr -n index.ndx -on numcont.xvg -group and selected
Thanks for your response, but
I've read the manual. What I realized is that, for example, I should consider
for every two, three or … atoms, a virtual atom. Here are some questions:
1 - Does not important consider which atoms together? or How much is the angle
between atoms?
2 -Does I need
Hi everybody,
I want to add a phosphate to my protein. Is this possible with gromacs?
Thank you
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can you be a bit more specific? Are you expecting to phosphorylate the
protein along the trajectory or did you want to run continuous simulations
with different phosphorylation states?
On 2012-09-03 09:30:58AM +0200, reising...@rostlab.informatik.tu-muenchen.de
wrote:
Hi everybody,
I want
Hi,
I have my protein without phosphorylations and now I want to phosphorylate
one residue of my protein.
Is this possible?
Thank you
can you be a bit more specific? Are you expecting to phosphorylate the
protein along the trajectory or did you want to run continuous simulations
with
You haven't anwsered my question. Did you just want to add the phosphate
before starting the simulation or were you hoping for the simulation to do it
for you?
On 2012-09-03 09:51:12AM +0200, reising...@rostlab.informatik.tu-muenchen.de
wrote:
Hi,
I have my protein without phosphorylations
Dear gmxers,
While I try to make one customed force field by studying some existing
force fields, I find that bond_type and at.num defining [atomtypes ]
in the ffnonbonded.itp are included in some force fields (i.e.
oplsaa), but not in other force fields (i.e gmx). I wonder how gmx
identifies the
I want to add the phosphor first.
And I hoped that there is a program just like the pdb2gmx which adds
hydrogens to the protein.
You haven't anwsered my question. Did you just want to add the phosphate
before starting the simulation or were you hoping for the simulation to do
it
for you?
You'll have to do it manually. Perhaps VMD or Chimera can help you with
adding the atoms to the initial pdb.
Then you'll have to create a modified amino acid topology for the amino acid
that is getting phosphorylated in your forcefield's .rtp file.
On 2012-09-03 10:05:08AM +0200,
2 sep 2012 kl. 20.47 skrev Smitty:
1) That .mdp applies different tables to K-K, protein-protein and all
other interactions, which isn't what you've said you've done.
3) Your life will be simpler if you use energygrp_table only for the
group-group interactions you want to change, and
On 9/3/12 2:04 AM, Raj wrote:
hi all,
I would like to measure the hydrophobic interaction of the ligand against
the protein during the simulation . From the forum I learnt g_mindist will
be the better tool. But when i used the command g_mindist -f traj.xtc -s
topol.tpr -n index.ndx -on
Hi Zifeng,
have you tried to use
g_tune_pme -npstring none …
Carsten
On Aug 20, 2012, at 5:07 PM, zifeng li lizife...@gmail.com wrote:
Dear Gromacs users,
Morning!
I am using Gromacs 4.5.4 version and tries to use the magic power of
g_tune_pme. However, it cannot be executed with the
Hi Chandan,
g_tune_pme also finds the optimal number of PME cores if the cores
are distributed on multiple nodes. Simply pass the total number of
cores to the -np option. Depending on the MPI and queue environment
that you use, the distribution of the cores over the nodes may have
to be specified
On 9/3/12 2:45 AM, fatemeh ramezani wrote:
Thanks for your response, but
I've read the manual. What I realized is that, for example, I should consider
for every two, three or … atoms, a virtual atom. Here are some questions:
1 - Does not important consider which atoms together? or How much
Hi Albert,
On Aug 25, 2012, at 7:37 AM, Albert mailmd2...@gmail.com wrote:
Dear:
Our institute got a IBM Power 775 cluster and it claimed to be very good.
However, it doesn't support g_tune_pme.
Are you shure that it is not supported? Maybe you just need the right syntax.
I use the
thank you justin ... I have given the entire protein as one group.. now will
it be ok or i need to give only hydrophobic resides alone as a index group.
Thank you once again for yor response
--
View this message in context:
On 9/3/12 7:47 AM, Raj wrote:
thank you justin ... I have given the entire protein as one group.. now will
it be ok or i need to give only hydrophobic resides alone as a index group.
Thank you once again for yor response
If you want hydrophobic contacts, you need index groups that specify
On 3/09/2012 6:02 PM, Wu Chaofu wrote:
Dear gmxers,
While I try to make one customed force field by studying some existing
force fields, I find that bond_type and at.num defining [atomtypes ]
in the ffnonbonded.itp are included in some force fields (i.e.
oplsaa), but not in other force fields
Erik Marklund wrote
2 sep 2012 kl. 20.47 skrev Smitty:
Why would you have 1-4 interactions for monoatomic species? Or between
different molecules for that matter?
---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
There is a G43a1 modification available with phosphorylated amino acids in the
users contribution section of the Gromacs homepage.
http://www.gromacs.org/Downloads/User_contributions/Force_fields
It was uploaded by Graham Smith and Justin made it compatible with the Gromacs
4.5.x versions, so
Hi,
Sometimes, I want to take a quick look at a certain property using one of
the Gromacs utilities. For example, I might want to use:
g_traj -f traj.trr -s topol.tpr -n index.ndx -nox -noy -b 5 -e 10 -ox
coord.xvg
to look at the z-component of the group specified in index.ndx from t = 5 ps
to
Have you tried to write to a named pipe? Like mkfifo coord.xvg then
g_traj -ox coord.xvg? Then tail -F coord.xvg?
I'm not sure this is less work than just letting it write the xvg and then
looking at the xvg (and deleting it later)...
On 2012-09-03 08:26:56PM -0400, Andrew DeYoung wrote:
Hi,
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