> A pressure without an error bar is a meaningless value. The fluctuations
> of pressure in most systems are on the order of tens or hundreds of bar,
> meaning your result is indistinguishable from the target value.
To help illustrate this, here is one example of the type of pressure
fluctuation y
Hello,
I noticed that gromacs has an environment variable that seems to allow it
to output neighbor lists. I haven't been able to figure out how to use it.
Does anyone have an example of how this could work?
Thanks,
Adriaan Riet
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Hello Tom,
I got something like decomposition errors when running in GPU clusters, and
later I found it is because of PBC unit cell angles. You can try to use
trajconv to get out of one pdb file from your simulation box. If the unit
cell is non-90degree, it will cause this domain decomposition err
Hi everyone,
I've recently gotten a simulation of a 2D crystal surface set up in
GROMACS using a combination of x2top and periodic-molecules. Things
run okay for me when I do small-scale tests on a single core
(minimization, NVT equilibration, etc), however when I try to scale
this up and
Dear Justin,
Thank you for your response. Yet, I have not been able to solve the problem.
The structure looks fine but gromacs is complaining about a dangling atom at
one of the terminal ends, if I choose no terminal to be added. While,
assigning a terminal to the ends (which I don't understand w
Hello Justin
I still don't understand where Gromacs takes the x coordinates in the output
pmf with g_wham
If I run g_wham with tpr-files and pullf-files without the pullx-files
-it tpr-files.dat -if pullf-files.dat
I get a profile which means that g_wham does not take the X-coordinates in the
p
Hi All,
Following is the structure of the molecule, which I wish to parameterize.
CH3 O
| ||
CH3 - C - O - C -
|
CH3
It is a peptide capping reagent. The last carbon will form bond with the
NH2 group of the peptide. I have generated the the topol
Dear Justin and Dallas
Thank you for your replying
I have another problem in minimizing and NVT run of my complex, including a
protein and a peptidic ligand which the ligand has 2 phosphotyrosine
residues. I generated a topology file of ligand using ff14sb in ambertools
16 and then converted the
Hello,
you can find information on how to extend simulations here:
http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html
Cheers
Paul
On 2018-11-08 14:23, Edjan Silva wrote:
Dear fellow scientists,
I'm doing a 40ns simulation between DNA and a small molecule. It
Dear fellow scientists,
I'm doing a 40ns simulation between DNA and a small molecule. It occurred
that around 30 nanoseconds, the computer hung up.
How do I start the simulation from the 30 nanoseconds performed?
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On 11/8/18 7:50 AM, Gonzalez Fernandez, Cristina wrote:
Dear Gromacs users,
In my simulations, I have specified ref_p= 1bar but after MD simulation I
obtain pressures equal to 0.19 bar (even
A pressure without an error bar is a meaningless value. The fluctuations
of pressure in most syste
On 11/8/18 5:20 AM, Rahma Dahmani wrote:
Dear Gromacs Users,
I want to run MD simulation of ligand in water box , for that i have
manually constructed a topology file of my ligand with antechamber tools
then i used GROMACS instructions to build a box of water molecules
(ligand_solv.gro), when
On 11/7/18 5:06 PM, Dallas Warren wrote:
Paper explaining dispersion correct, and what it is:
http://dx.doi.org/10.1021/jp0735987
And note that not all force fields are parametrized in such a way that
they make use of dispersion correction.
-Justin
Catch ya,
Dr. Dallas Warren
Drug Del
On 11/7/18 2:46 PM, daniel madulu shadrack wrote:
Dear, I want to combine proteins to merge into single pdb but I get this
error below.
Command line:
gmx trjcat -f 10ns.pdb 15ns.pdb 40ns.pdb 60ns.pdb 90ns.pdb -o all.pdb
You don't need trjcat, just use the standard Linux cat to combine t
On 11/7/18 1:05 PM, Ali Khodayari wrote:
Dear gmx users,
I am trying to simulate a cellobiose, using GROMOS53a6CARBO. The atom names
were modified according to the rtp file of the force field. Yet, I get the
following error while I perform pdb2gmx command:
Fatal error:
Residue 4 n
Dear Gromacs users,
In my simulations, I have specified ref_p= 1bar but after MD simulation I
obtain pressures equal to 0.19 bar (even with long simulation times) when using
pcoupl=Parrinello-Rahman. I know that Parrinello-Rahman is recommend for
production runs and Berendsen for NPT equilibrat
Dear Gromacs Users,
I want to run MD simulation of ligand in water box , for that i have
manually constructed a topology file of my ligand with antechamber tools
then i used GROMACS instructions to build a box of water molecules
(ligand_solv.gro), when i tried to minimize my structure (with grompp
Hi Mark,
Thank you for your answer. I didn't know this option. From what I have
read, eneconv is for reading parameters for Nose-Hoover or
Parrinello-Rahman coupling. Thus, if I am doing first an NVT simulation
with the velocity-rescale thermostat or a Langevin dynamics, I don't need
the .edr file
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