Hi everyone,
How does one go about preparing a polymer in a given state of tacticity?
>From what I understand about tacticity in polymers, it boils down to
coefficients(C1,C2,C3,C4,C5,C6) in Ryckaert-Bellemans function. If the
potential well is not deep enough, the polymer can easily transition fr
Dear all,
I am setting up a system where I want the solute to be immersed in a
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to be at say
T1 and T2 kelvins. The rest of the system will not be subjected to a
thermost
I am trying to test the reproducibility of the md production run.
You can use the options
gen-vel = yes
gen-temp = 300
gen-seed = -1
in your .mdp file and run again. That example will generate new random
velocities corresponding to 300 K and u
Hi Gromacs folks,
I am trying to test the reproducibility of the md production run. Should I
use the product from the previous MD run as the starting structure and run
it with the same mdp files, or just simply do a re-run with all the same
mdp files from the original pdb file?
Thanks in advance,
M
Never mind my previous question about using trjconv for fitting in
RMSD calculations. It does produce identical results compared to using
gmx rms alone. I just had a subtle error in atom numbering, which
resulted in bogus RMSD values.
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I have done simulation that have HIS in binding site, so I run 2 simulation
one with HIE and the other is HID and then I will check is there any
difference (hydrogen bond) between 2 simulations and then decide which
protonation state of HIS should be employed. You can try in that way
On Thu, Jul 5
Hi Gromacs folks,
I am trying to re-run a 100 ns simulation with different velocities and
random seed. Would the setup from the mdp file as the following a good one?
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp= 300 ; temperature f
Dear Gromacs developers
For the latest Gromacs version (GROMACS 2018.2) available, energy group
exclusions do not support by the verlet cutoff scheme (The group cutoff scheme
supports the energy group exclusions,but it is inconvinent to use). So is there
a time table when energy group exclusio
I ran into what seems to be a bug, namely that the -skip option in gmx
rms doesn't seem to do anything. The output always has the RMSD values
for all frames, even if -skip is specified. I filed a bug
(https://redmine.gromacs.org/issues/2565).
Then I resorted to trjconv to do the skipping be
Hi Raag,
Within your .mdp file there is a "Run parameters" section that has the
following line items (see below). If you want to achieve 500 ns you need to
increase the nsteps and multiply it times the timestep - ensuring that the
timestep is appropriate enough for what you want to achieve. See
On 7/5/18 8:50 AM, antonia vyrkou wrote:
Hello,
I am using GROMACS 5.1.4 and while trying to convert a .pdb file to .gro I
get the error message
“Fatal error:
Atom HD1 in residue HIS 66 was not found in rtp entry HIE with 17 atoms
while sorting atoms.”
Is it not possible to treat some HI
Hello,
I am using GROMACS 5.1.4 and while trying to convert a .pdb file to .gro I
get the error message
“Fatal error:
Atom HD1 in residue HIS 66 was not found in rtp entry HIE with 17 atoms
while sorting atoms.”
Is it not possible to treat some HIS molecules as HID (where HD1 exists)
and do
If I am not wrong, you are suggesting the "per mol" in KJ/mol is total number
of particles in the system. Which in special case for pure component system
should give per particle energy scaled by Avogadro number, so for my case the
RMSD decrease by (N)^1/2 should come out to be same whether I us
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