Dear Nilesh,
If memory serves me right, it computes the HB autocorrelation function based on
all individual HBs, then fits Luzar and Chandler’s kinetic model to that (for
now).
Kind regards,
Erik
Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College
Department of
Dear Gromacs Users,
I am calculating hydrogen bond life time for water system. I have 128
water molecules in the system. The program scan the HB criteria for each
OH bond with the rest 127 oxygen (128*128).
For single OH bond I have calculated the HB lifetime. If there are more
than 1 HB how
Hi all,
I am a new user to gromacs and I want to calculate vector (Z-axis) position
for centre of mass of a ligand in lipid simulation throughout the
simulation of 50 ns. Is there any other way to calculate the position of
the ligand (Z- position) through out the simulation.
Any help will be
Hi,
gmx traj seems like the tool for you.
Kind regards,
Erik
Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College
Department of Chemistry
Physical Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ
On 3 Jul 2015, at 15:55, Him
Dear Gromacs users,
I am trying to generate topology for a membrane protein, which is capped
with acetyl and methyl amide group, using Charmm36 force field in Gromacs.
Unfortunately, the acetyl (ACE) group is seems to be missing in the Gromacs
Charmm36 force field. Can anybody suggest me a way to
Dear Gromacs users,
I am working with membrane proteins. I have generated the membrane-protein
system ( contains lipids, protein, water and ions) with some specification.
For eg., I have positioned few ions and water molecules at particular
location using some in-house programs. Now, I would
On 7/3/15 7:56 AM, anu chandra wrote:
Dear Gromacs users,
I am working with membrane proteins. I have generated the membrane-protein
system ( contains lipids, protein, water and ions) with some specification.
For eg., I have positioned few ions and water molecules at particular
location
On 7/3/15 11:10 AM, anu chandra wrote:
Dear Gromacs users,
I am trying to generate topology for a membrane protein, which is capped
with acetyl and methyl amide group, using Charmm36 force field in Gromacs.
Unfortunately, the acetyl (ACE) group is seems to be missing in the Gromacs
Charmm36
Well, once it was clear that the speed-up wasn't exceptionally high, I assumed you wouldn't be interested in the complete logs. There's also the additional complication of having no access to file sharing services from where I work. :)
Alex
SP The full context is provided by the
On 7/3/15 2:09 AM, soumadwip ghosh wrote:
Dear Justin and Mark,
I have written a tentative reply to the
reviewer
where I have mentioned the works ( DPPC membrane, protein unfolding
and so on) where different objectives have been met with upon varying
People do this all the time, e.g.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114152
Unfortunately, the models and the resulting data are worth very
little, because the simulated nanoparticles arent't made of metal.
They are blobs of van der Waals particles, instead.
The
Thank you Alex for the comprehensive reply.
On Saturday, July 4, 2015 1:12 AM, Alex nedoma...@gmail.com wrote:
People do this all the time, e.g.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114152
Unfortunately, the models and the resulting data are worth very
Dear Seema,
You do not need to run the simulation anew, you can make use of mdrun -rerun,
which uses an existing trajectory but a new tpr file, with new energy groups
for instance.
That said, it is often impossible to decompose the energy exactly into separate
contributions from, say,
Dear Sathish,
Do you actually pull it 20 nm from the DNA, or is your plot showing the wrong
units? If that is correct, you have very long-reaching effective interactions
in your system. How big is your nanoparticle?
Kind regards,
Erik
Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford
Dear gromacs-users,
Sorry in previous the attached link was not
working. I have run umbrella samplling for RNA and nanoparticle. For this
system, I got the PMF in which there is no plateau value and it has
constant minimum value. in the last window of umbrella
Thank you for your kind reply.
I pull the RNA from one end of the strand away from nanoparticle.
Nanoparticle contains 200 atoms. The distance between center of mass of
nanoparticle and RNA in last window is 20 nm only.
Best
sathish
On Fri, Jul 3, 2015 at 1:25 AM, Erik Marklund
Yes I have pulled upto 20 nm. The distance between final nanoparticle and
one end of the RNA is 48 nm. Total box size is 12 50 12. And there is no
periodic image interactions also. Please tell me what could be the reason
in this case.
Thanks
sathish
On Fri, Jul 3, 2015 at 1:30 AM, Sathish Kumar
Dear Justin and Mark,
I have written a tentative reply to the
reviewer
where I have mentioned the works ( DPPC membrane, protein unfolding
and so on) where different objectives have been met with upon varying
concentrations and it seems that the force fields just do
Dear all,
I would like to find out the distribution of molecules above a flat surface,
such as the surface of a membrane. Would it be appropriate to be using:
gmx rdf -f run.xtc -s run.tpr -n index.ndx -surf mol -rdf mol_com -pbc
After staring at the manual for really long, I can't quite figure
Hi,
What is your pull geometry, and is your RNA periodic or somehow kept aligned
with the x or z axes?
Erik
On 3 Jul 2015, at 09:50, Sathish Kumar
sathishk...@gmail.commailto:sathishk...@gmail.com wrote:
Yes I have pulled upto 20 nm. The distance between final nanoparticle and
one end of the
Dear Gromacs-Users,
I want to do a gromacs installation with intermolecular bonded interaction
support to apply a weak repulsive potential between ligands to avoid
aggregation. All of the patches in this URL (
https://gerrit.gromacs.org/#/c/2566/) were added or replaced with original
files in
Hi,
On Fri, Jul 3, 2015 at 12:48 PM Hassan Aaryapour hassan.grom...@gmail.com
wrote:
Dear Gromacs-Users,
I want to do a gromacs installation with intermolecular bonded interaction
support to apply a weak repulsive potential between ligands to avoid
aggregation. All of the patches in this
On 3 Jul 2015, at 11:31, Erik Marklund erik.markl...@chem.ox.ac.uk wrote:
Hi,
What is your pull geometry, and is your RNA periodic or somehow kept aligned
with the x or z axes?
… and is your nanoparticle charged?
Erik
Erik
On 3 Jul 2015, at 09:50, Sathish Kumar
Pull geometry = distance,
Pull rate = 0.005 nm/ps
RNA is aligned along Z-axis. it is not periodic.
On Fri, Jul 3, 2015 at 3:31 AM, Erik Marklund erik.markl...@chem.ox.ac.uk
wrote:
Hi,
What is your pull geometry, and is your RNA periodic or somehow kept
aligned with the x or z axes?
Erik
Dear all,
I pulled a protein using pdc=xyz, and want to do unloading simulation. The
problem is both ends of the protein run out of the boundary after pulling.
After unloading for a while, I found that both ends did not connect to where
they should connect.
Is there a way that I can
Yes it is positive chargedIt has 48 + charges and RNA has 44 negative
charges.
On Fri, Jul 3, 2015 at 3:38 AM, Erik Marklund erik.markl...@chem.ox.ac.uk
wrote:
On 3 Jul 2015, at 11:31, Erik Marklund erik.markl...@chem.ox.ac.uk
wrote:
Hi,
What is your pull geometry, and is your
Dear Gromacs users,
I am working with membrane proteins. I have generated the membrane-protein
system ( contains lipids, protein, water and ions) with some specification.
For eg., I have positioned few ions and water molecules at particular
location using some in-house programs. Now, I would
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