Dear all,
Can any one help e regarding
1.) I want to find the binding energy of ligand with the protein , and
2.) Hydrogen Bond energy of the protein ligand interactions (for
H-bond ).. and
3 ) if possible H bond distances along the time scale(say 10ns).
Is there any way
4 ) to measure the
Hi everybody,
I want to put my protein in the box with editconf but when I look at it it
is always at the border of the box and not at the center. I tried it with
those two commands:
editconf -f 3m71.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330
-c -bt dodecahedron -d 1.0 2logErr
On 7/3/12 5:10 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to put my protein in the box with editconf but when I look at it it
is always at the border of the box and not at the center. I tried it with
those two commands:
editconf -f 3m71.gro -o 3m71_box.gro
On 7/3/12 2:24 AM, Ravi Raja Merugu wrote:
Dear all,
Can any one help e regarding
1.) I want to find the binding energy of ligand with the protein , and
Umbrella sampling or free energy calculations can determine binding energies.
2.) Hydrogen Bond energy of the protein ligand
Hi everybody,
I wanted to do a minimization with mdrun but the only output I get is:
3m71_minim.edr
3m71_minim.log
3m71_minim.trr
But no structure file like .pdb i.e.
There was no error in the step before where I prepared the input file with
grompp. My .mdp file looks like this:
define
On 7/3/12 5:40 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I wanted to do a minimization with mdrun but the only output I get is:
3m71_minim.edr
3m71_minim.log
3m71_minim.trr
But no structure file like .pdb i.e.
There was no error in the step before where I prepared
Ah okey,
Thank you!
On 7/3/12 5:10 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to put my protein in the box with editconf but when I look at it
it
is always at the border of the box and not at the center. I tried it
with
those two commands:
editconf -f
Hi everybody,
is it correct when I set the
nstep = -1 and
emtol = $number
that the minimization goes as long as the energy difference between the
previous step and this step is not lower as $number. And that there is no
maximal stepsize?
Bests,
Eva
--
gmx-users mailing list
On 7/3/12 8:11 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
is it correct when I set the
nstep = -1 and
emtol = $number
that the minimization goes as long as the energy difference between the
previous step and this step is not lower as $number. And that there is no
Ah okey. Yes sorry that was a typo...I ment nsteps.
So but is there a possibility to define a minimal step size so that the
minimization ends when the energy does not changes much any more?
On 7/3/12 8:11 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
is it correct
Dear Gmx Users,
Do you know or can you suggest some results based on the comparison of
the force constant in Umbrell Sampling? Any literature?
As far as I understand when you use the same staring coordinates (from
the same pulling simulation) for windows but you just change the force
constant
Dear all,
I know several questions about implict solvent have already been asked in this
list. I think and hope the question I have has not been raised. Forgive me if I
am wrong.
I have read that all-to-all kernels are the best option when doing implicit
solvent. Otherwise one should use large
On 7/3/12 8:57 AM, Ramon Crehuet Simon wrote:
Dear all,
I know several questions about implict solvent have already been asked in this
list. I think and hope the question I have has not been raised. Forgive me if I
am wrong.
I have read that all-to-all kernels are the best option when doing
On 7/3/12 8:41 AM, Steven Neumann wrote:
Dear Gmx Users,
Do you know or can you suggest some results based on the comparison of
the force constant in Umbrell Sampling? Any literature?
That would be lovely, but I've never seen such a thing. One could probably
write a book with all the
On 7/3/12 8:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Ah okey. Yes sorry that was a typo...I ment nsteps.
So but is there a possibility to define a minimal step size so that the
minimization ends when the energy does not changes much any more?
Just set emtol to some
On Tue, Jul 3, 2012 at 2:04 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/3/12 8:41 AM, Steven Neumann wrote:
Dear Gmx Users,
Do you know or can you suggest some results based on the comparison of
the force constant in Umbrell Sampling? Any literature?
That would be lovely, but I've
I'm performing a verification of the energy dissipation of a single atom,
thermally coupled to a heat drain (or sink). In other words, the Langevin
equation of motion is d/dt v(t) = - gamma * v(t).
If using the Stochastic Dynamics integrator I do indeed get dissipation,
however if
Dear users,
I use gromacs version 4.5.4 and is building residues of my own polymer which
has a ester group (COOR). Should I consider the ester as one neutral
group or split it into two groups( -COO and -R) ?
Here's some information I find:
1. Should consider them as one group. Based on the fact
Hi all,
I am calculating SAS using g_sas of my system (several peptides in
water and ions, Na and Cl). I choose:
for calculation group: non-water
for output group: protein
(400 out of 750 atoms were classified as hydrophobic)
When I plot the Area vs time graphs, both the
On 7/3/12 10:49 AM, Turgay Cakmak wrote:
Hi all,
I am calculating SAS using g_sas of my system (several peptides in
water and ions, Na and Cl). I choose:
for calculation group: non-water
for output group: protein
(400 out of 750 atoms were classified as hydrophobic)
Dear Christopher Neale,
Let me re-frame my question again.
Though I am new to US, but I have a basic idea about performing US. My
main query lies for these 2 H-bonds: one between Protein and MG and
other one between protein and GTP.
I want to know if I can perform umbrella sampling to explain
Dear Stephan Watkins,
Thanks for your response. I would again like to specify my query to my
main concerns. My main query lies for the 2 H-bonds: one between
Protein and MG and
other one between protein and GTP.
1) I have 2 configurations of my system. In the initial state:
Prot-Mg-GTP complex
As a side note:
The rupture process is a stochastic process, so a single rupture force
is meaningless, since it is a distributed property. So you need to do
many simulations to get the distribution / average rupture force.
It that same like equilibrium properties, one doesn't determine them
You have 1mol of your system.
conversition factor for
kJ/(mol*nm) - pN is approx 1.661
Am 29.06.2012 10:33, schrieb gmx-users-requ...@gromacs.org:
Dear Gmx Users,
How to recalculate the force constant from the harmonic potential: 1
[pN/A] into [kJ/mol nm2] ? Where is the [mol] here?
think you encounter the problem, that you construct your pmf from a 3d
simulation and project it onto 1d, but do no correction.
For TI (if you constrain the distance in all three directions) the pmf
is given by
V_pmf(r) = - \int [ F_c + 2/(beta*r) ] dr
with F_c the constraint force and \beta
On 7/3/12 2:50 PM, Thomas Schlesier wrote:
think you encounter the problem, that you construct your pmf from a 3d
simulation and project it onto 1d, but do no correction.
For TI (if you constrain the distance in all three directions) the pmf is given
by
V_pmf(r) = - \int [ F_c + 2/(beta*r) ]
It also depends in some cases strongly on the system.
I have a two-state system in which both states are rather narrow (doing
a normal pulling simulation, the end-to-end-distance seems nearly
constant). In these two regions one could use small force constants. but
both state are seperated by a
ok, had still the 4.0.x version in mind, there the .tpr-files were not used.
could be that the factor was introduced in 4.5.x, but i don't think so.
If there would be steric crashes, which would account for the strong
increase in the PMF, one should see them in the force profile.
for more
You neglected to mention what Force Field you are using.
See Also: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060752.html
On 2012-07-03 10:47:25AM -0400, zifeng li wrote:
Dear users,
I use gromacs version 4.5.4 and is building residues of my own polymer which
has a ester group
Hello community,
I'm trying to create a topology for a molecule using the MARTINI force
field which is a coarse-grain (CG) forcefield. I understand that to
optimize the bonded parameters, one needs to model the AA version and
extract the equilibrium angle and force constants. As is said in the
Gromacs Users,
I am interested in implementing a thole polarization scheme in my
simulations of ionic liquids. However, the gromacs 4.5 manual does
not give much information on this feature beyond a brief mentioning.
An example of the implementation can be found in the mailing list at
On 07/03/2012 11:01 PM, Justin A. Lemkul wrote:
On 7/3/12 8:57 AM, Ramon Crehuet Simon wrote:
Dear all,
I know several questions about implict solvent have already been
asked in this list. I think and hope the question I have has not been
raised. Forgive me if I am wrong.
I have read that
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