Hello everyone,
I am simulating a coarse-grained model of a membrane protein (GPCR) in
lipid bilayer and an all-atom ligand octopamine. I build the protein,
solutes, and membrane in the web server CHARMM-GUI. While, I added the
ligand to the protein complex manually using the same coordinates of t
Hi,
Off topic for this discussion, but what would people think if we changed
things around so that grompp would do that constraining, before writing the
tpr file?
This will mean that the configuration in the tpr does not always match the
configuration that was given to grompp, but instead matches
Dear gmx comunity,
I am trying to calculate the electrostatic interaction of my system for
force field development. My system consists of 7 positively charged
particles interacting (system A) with another positively charged particle
(system B). I calculate the electrostatic interaction by doing re
Hi,
The standard output of the first set of runs is also something I was
interested in, but I've found the equivalent in the
complex/TESTDIR/mdrun.out files. What I see in the regresiontests output is
that the forces/energies results are simply not correct; some tests simply
crash after 1-2 steps,
Hi,
The negative energy is due to the uniform background charge that appears when
your system has a net charge, not due to shifting of pair interactions.
Computing the absolute energy of a periodic system with net charge is
meaningless.
Cheers,
Berk
From: gr
Hi all,
I ran some CG simulations of a protein inserted in a lipid bilayer, with
several lipids. I used the msd tool to compute the lipid (using the PO4)
diffusion coefficient. For one of the lipid I got D = 0.6 x 10^-5
cm^2/s, which is 600 um^2/s. According to the Martini website "To
compare
Dear Sergio,
If you're using PME, you need to also include the reciprocal contribution.
Gerrit
Dear gmx comunity,
I am trying to calculate the electrostatic interaction of my system for
force field development. My system consists of 7 positively charged
particles interacting (system A) with
On 3/29/19 3:32 AM, Mac Kevin Braza wrote:
Hello everyone,
I am simulating a coarse-grained model of a membrane protein (GPCR) in
lipid bilayer and an all-atom ligand octopamine. I build the protein,
solutes, and membrane in the web server CHARMM-GUI. While, I added the
ligand to the protein
On 3/29/19 4:30 AM, Mark Abraham wrote:
Hi,
Off topic for this discussion, but what would people think if we changed
things around so that grompp would do that constraining, before writing the
tpr file?
This will mean that the configuration in the tpr does not always match the
configuration
Dear Gromacs Developers and Users,
I need a small help in GROMACS trajectory analysis. I want to define a
selection i.e., 4Ang volume around two residues (from different chains X and
chain Y ) that make your binding site --- Within this selection I want count
number of waters molecules along th
Thank you Professor Lemkul,
But would you suggest on how can I coarse-grained the ligand I am using? I
have been searching resources online but they do not work in our part.
I hope you can help us. Thank you Prof. Lemkul!
Best regards,
Mac Kevin E. Braza
On Fri, Mar 29, 2019, 8:59 PM Justin Lem
Hello,
Thanks for the quick reply, I am not sure if you are referring to this term
of the Ewald Sum:
V_0 = ( f*beta ) * SUM(q_i^2) / sqrt(pi)
Since the sum of the square of the charges of the system (AB) is the same
as the sum of the square of the charges of the system (A) plus the same
from sys
I mean the q_tot^2 term.
This attractative term goes with the square of the total charge, so has larger
magnitude for AB than A+B, so the result in negative.
Berk
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Sergio Perez
Sent: Friday,
Great! So I just have to discount this term to obtain the positive energy
expected.
Thank you very much!
Sergio
On Fri, Mar 29, 2019 at 4:11 PM Berk Hess wrote:
> I mean the q_tot^2 term.
> This attractative term goes with the square of the total charge, so has
> larger magnitude for AB than A+B
Thank you all for the help!
Introducing the h-bond constraints into the minimization as well, did reduce
the magnitude of the initial jump to 10.1 kJ per mole in the first 0.0066 ps
but did not remove the problem entirely. I am also using different
coulombtype's in the minimization (Cut-off) an
On 3/29/19 12:23 PM, Kruse, Luke E.(MU-Student) wrote:
Thank you all for the help!
Introducing the h-bond constraints into the minimization as well, did reduce
the magnitude of the initial jump to 10.1 kJ per mole in the first 0.0066 ps
but did not remove the problem entirely. I am also usin
On 3/29/19 9:17 AM, Mac Kevin Braza wrote:
Thank you Professor Lemkul,
But would you suggest on how can I coarse-grained the ligand I am using? I
have been searching resources online but they do not work in our part.
I don't work with CG simulations, so I'm not much help. I would think
tha
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