Dear users,
I am working on ctab/water surfactant system and got stuck with the
calculation of tilt angle distribution of hydrocarbon chain. Is there any
tool to calculate the tilt angle distribution in gromacs. Please specify
the way to do that...
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Gromacs Users mailing list
* Please search t
Dear all
I RUN MOLECULAR SIMULATION FOR DNA-SMALL MOLECULE COMPLEX (50 NS), I
WANT TO ANALYSIS USING MMPBSA, FOR POLAR SOLVATION ENERGY CALCULATION ,
I USED THE MMPBSA.MDP [1] OBTAINED FROM
HTTPS://RASHMIKUMARI.GITHUB.IO/G_MMPBSA/HOW-TO-RUN.HTML.
I THINK THERE IS SOME PROBLEM, BECAUSE AFT
Dear all,
I have a protein_Ligand complex which I want do Umbrella Sampling on it to
find out free energy.for this purpose I used Justin tutorial(Tutorial 3:
Umbrella Sampling: GROMACS Tutorial ).
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GROMACS Tutorial
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Here is my questiones:in tutorial he said:
Acetyl
Hi all,
A quick question -- I just wanted to double check that the Coulomb-SR term
does NOT include the Coulomb-14 term.(To me, the "SR" label is somewhat
misleading as it makes me think that it includes "everything" short
ranged).
In other words, if one wishes to know the total Coulombic en
On 5/28/19 7:49 AM, Mala L Radhakrishnan wrote:
Hi all,
A quick question -- I just wanted to double check that the Coulomb-SR term
does NOT include the Coulomb-14 term.(To me, the "SR" label is somewhat
misleading as it makes me think that it includes "everything" short
ranged).
In othe
thank you!
Mala
On Tue, May 28, 2019 at 8:01 AM Justin Lemkul wrote:
>
>
> On 5/28/19 7:49 AM, Mala L Radhakrishnan wrote:
> > Hi all,
> >
> > A quick question -- I just wanted to double check that the Coulomb-SR
> term
> > does NOT include the Coulomb-14 term.(To me, the "SR" label is
> s
Dear all,
Any comment on this, please?
Thank you.
Alexander
On Thu, May 23, 2019 at 10:02 AM Alex wrote:
> Dear GMX user,
> I have a 110 GB trajectory from which I would like to extract only the
> trajectory of the part of my interest, the rest is water. To do so, I use "
> echo 1 | mpiexec_mpt
Hi,
You can use trjcat
On Tue 28 May, 2019, 6:10 PM Alex, wrote:
> Dear all,
> Any comment on this, please?
>
> Thank you.
> Alexander
>
> On Thu, May 23, 2019 at 10:02 AM Alex wrote:
>
> > Dear GMX user,
> > I have a 110 GB trajectory from which I would like to extract only the
> > traject
Hi all,
I’m running GROMACS to simulate a simple phospholipid bilayer membrane
(POPC) under deformation, and plot the von Mises stress-strain curve to
determine yielding point.
I have got the membrane deformed and extractred output pressures from .edr
file (option PRESS X, PRESS Y, PRESS Z) to
Hi all,
In GROMACS Manual, it is said that "In most cases Parrinello-Rahman
barostat would be combined with the Nose-Hoover thermostat as the most
practical choice", and I see that Nose-Hoover algorithm is only available
for temperature coupling, not pressure coupling. Why is Nose-Hoover not
used
Hi,
Why should it be used? :-)
Mark
On Tue, 28 May 2019 at 23:28, Anh Vo wrote:
> Hi all,
>
> In GROMACS Manual, it is said that "In most cases Parrinello-Rahman
> barostat would be combined with the Nose-Hoover thermostat as the most
> practical choice", and I see that Nose-Hoover algorithm i
Hi,
On Tue, 28 May 2019 at 23:26, Anh Vo wrote:
> Hi all,
>
>
> I’m running GROMACS to simulate a simple phospholipid bilayer membrane
> (POPC) under deformation, and plot the von Mises stress-strain curve to
> determine yielding point.
>
>
>
> I have got the membrane deformed and extractred out
I am calculating the free energy change in transforming one small molecule
into another by the simple removal of a CO2 from the first molecule, and
also mutating some bond parameters slighty since the second molecule has a
couple different atom types in GAFF without the CO2 attached to it.
I analy
Hello gromacs users,
Is there a reason why segmentation fault appeared when gmx hbond command was
used?
Thank you,
Neena
From: Neena Susan Eappen
Sent: Friday, May 24, 2019 12:40 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Segmentation
Hi all,
How did you choose your timestep and simulation time when running GROMACS?
Is there any logic for deciding that?
I’ve read that larger time step permits better sampling without significant
errors in observed thermodynamic, structural or dynamic properties => What
does “sampling” mean? Why
Hi,
That totally depends on your forcefield. Most classical all-atom
forcefields are recommended to be run with a 2 femtosecond timestep.
Some coarse-grained forcefields like Martini can do 20+ fs, but you’ll
want to check the literature.
As for better sampling, you simply sample longer times for
Hi all,
I'm new to GROMACS and there are some terms that I’m not very clear when
reading GROMACS materials. I have looked them up and read more but I’m
still confused. Please help me to clarify them.
- What is improper vs. proper dihedral?
- It is said that “If a dynamical system i
Proper dihedrals deal with rotation around a bond i.e. for a chain
C-C-C-C, the proper dihedral will encodes the potential energy versus
angle curve for the rotation around the central -C-C- bond.
From the GROMACS Manual
http://manual.gromacs.org/current/reference-manual/functions/bonded-interacti
Would be a good idea to provide the exact command line used, and a
copy of the exact output from the command. Copy and paste the text,
don't type it out from memory.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
Hi,
I'm still not clear what "sampling" means. Does it mean collecting data
from the simulation?
Thank you very much for your answer.
Best,
Anh Vo
-Original Message-
>
>
> Message: 4
>
> Date: Tue, 28 May 2019 20:43:32 -0400
>
> From: Kevin Boyd
>
>
>
> Hi,
>
>
>
> That totally depe
Hi,
2. As I know, lower yield stress means the molecules are not holding
together in the structure as well, and higher yield means that some change
is happening later in GROMACS simulations. Together, they suggest that your
chains are not pulling away from one another as quickly. In other words,
t
Hi,
Previously, as my colleague performed the same simulation with me (POPC
bilayer membrane under equibiaxial tension) in LAMMPS, he could use
Nose-Hoover for both temperature and pressure coupling. But in GROMACS when
I tried to re-do what he has done, I could not use Nose-Hoover for pressure
co
Different simulators use different thermostats and barostats, and given
that molecular simulations are a lot like grandma's cooking, there is no
truly clear answer to your question. However, I do have a few
suggestions. If you want to recreate exactly what your colleague did,
use LAMMPS -- its
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