Dear users,
I am trying to do NMA
First i did energy minimization using .mdp file with conjugate gradient
method,
Next i calculated hessian matrix by using integrator = nm
Then i calculated the eigen vectors from 7 to 100 using g_nmeig
to analyze eigen vectors i use the
from the eigenvectors with
g_nmens.
Cheers,
Tsjerk
On Mon, Nov 25, 2013 at 5:05 PM, Sathish Kumar sathishk...@gmail.com
wrote:
Dear users,
I am trying to do NMA
First i did energy minimization using .mdp file with conjugate gradient
method,
Next i
Dear users,
I am trying to do NMA
First i did energy minimization using .mdp file with conjugate gradient
method,
Next i calculated hessian matrix by using integrator = nm
Then i calculated the eigen vectors from 7 to 100 using g_nmeig
to analyze eigen vectors i use the
Hai
I have done simulation of DNA on carbon nano tube surface. I want
to calculate structural changes (means changes in stacking, puckering
angles and bending of helix) in DNA. Can any suggest me how to calculate
these things.
Thank You Very Much.
regards
M.SathishKumar
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Gromacs
Hai
I am trying to calculate torsional angles in DNA, for that first I
made angle.ndx file by using
mk_angndx -f prod.tpr -n angle.ndx -type dihedral
the out put angle.ndx is looks like as following
[ Phi=0.0_3_1.31 ]
12 2 3 412 2 31512 2 3
Hai gromacs users
I am running umberalla samplling simulations. How can I determine the
suitable force constant and pulling rate for my system.
Thanks
sathish
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So in SiO2 structure atoms are getting merged, is that the reason for the
error in simulation?
On Fri, Sep 12, 2014 at 6:57 AM, Mirco Wahab
mirco.wa...@chemie.tu-freiberg.de wrote:
On 12.09.2014 13:30, Sathish Kumar wrote:
And here i attached the md.log file and em.gro file. Please once
Hai
I run the umbrella sampling with the help of tutorial of
justinIn my system rna is binding with gold nanoparticle...to find out
the binding energy i run the umbrella sampling using the space 0.2 nm and i
got total 59 configurations, each configuration was run for 5 ns. The
profile
Add the parameters for LIG residue in force filed. In that give information
about the LIG in
rtp file
nonbonded file
bonded file
I think then it will work.
On Mon, Sep 22, 2014 at 5:46 AM, marcello cammarata mstaxmarce...@yahoo.it
wrote:
Hi,
i had checked all the archives, i have read about
Dear gromacs usres,
I have run the umbrella sampling with the help of tutorial of justinIn
my system rna is binding with gold nanoparticle...to find out the binding
energy, i run the umbrella sampling by pulling one end of the siRNA untill
it unbind from gold nanoparticle. The snap shots
Dear gromacs usres,
I have run the umbrella sampling with the help of tutorial of justin. In
my system rna is binding with gold nanoparticle. To find out the binding
energy, i run the umbrella sampling using the space 0.1 nm and i got total
79 configurations, each configuration was run for 5 ns.
the umbrella don't overlap enough at those z ?
Can you make an overlay plot of the histograms of each umbrella?
On Mon, Oct 13, 2014 at 1:54 AM, Sathish Kumar sathishk...@gmail.com
wrote:
Dear gromacs usres,
I have run the umbrella sampling with the help of tutorial of justin. In
my system rna
I am not able to find wheather the windows are overlaped or not. Please
help me in this.
Thanks.
On Mon, Oct 13, 2014 at 10:05 AM, Sathish Kumar sathishk...@gmail.com
wrote:
Hai
Yes, I have ploted the histogram, all windows are merged..please
check this histo.jpg file attached
me. And please suggest
me how to solve this problem.
Thanks
sathish
On Mon, Oct 13, 2014 at 10:08 AM, Sathish Kumar sathishk...@gmail.com
wrote:
I am not able to find wheather the windows are overlaped or not. Please
help me in this.
Thanks.
On Mon, Oct 13, 2014 at 10:05 AM, Sathish Kumar
Dear gromacs-users,
I have run the umbrella sampling with the help of
tutorial of justin. In my system rna is binding with gold nanoparticle. To
find out the binding energy, i run the umbrella sampling using the space
0.1 nm and i got total 79 configurations, each
Hai gromacs users,
Can we use the direction-periodic mdp option
while running the samplling of windows instead of distance. The distance
option was giving error that
Distance of pull group 1 (15.017257 nm) is larger than 0.49 times the box
size (15.033495) .
So, for
Dear gromacs users,
I have seen one paper in that ionic
currents were calculated using NAMD. The ionic currents calculated for the
systems contain single peptide, dimer and trimer along with 1 M NaCl. Based
on the changes in the ionic current, the size of the
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
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 08:28, Sathish Kumar sathishk...@gmail.com wrote:
Dear gromacs-users
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
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 RNA is 48 nm. Total box size is 12 50 12. And there is no
periodic image interactions also. Please tell me
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 sathishk...@gmail.commailto:
sathishk...@gmail.com wrote:
Yes I have pulled upto 20 nm. The distance between final nanoparticle and
one
Hai gromacs users
I am trying to run the simulation of rna with
urea as solvent. I have added 300 molecules of water using genbox command
and while runnning the energy minimization step, the total potential energy
is coming as positive. please help me to solve this
Hi all,
I have calculated electrostatic interaction energy between poly alanine
peptide and nanomaterial using columb SR term. The nanomaterial has partial
charges and peptide also. But the calculated electrostatic interaction
energy with peptide is around 0.3 kJ/mol. Is this values are correct?
velocities.
And I have seen the mdout.mdp file which created during generation of
npt.tpr, in that gen_seed = 173529. In npt.mdp file, I have not used
gen_seed option. Can anyone please explain me why it is showing like this?
Thanks
Sathish
On Tue, Sep 20, 2016 at 11:52 PM, Sathish Kumar
want to have different initial velocities, use gen_seed =
> -1 at will.
>
> Best regards,
> João
>
>
>
> On Wed, Sep 21, 2016 at 3:22 PM, Sathish Kumar <sathishk...@gmail.com>
> wrote:
>
> > Dear gromacs-users
> >
> >
Dear gromacs-users,
I want to run simulation of system of
peptide with carbon nanotube. And I want to run multiple simulations for
the same initial structure using different random initial velocities. For
that which values I have to use in the case of
Dear Justin
Thank you very much for your reply. So, Is that I can use gen_seed=5,
gen_seed=10 to assign different initial velocities for the same initial
structure?
Thanks
Sathish
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