I’m new to Gromacs but I have been doing large-scale calculations for many
years. I believe that most changes to Gromacs are well-documented in the
release notes for each patch or version update. I would start there to see if
you can find an explanation for the different results you obtained.
Dear All,
I am using Gromax 2019 and running an umbrella sampling for two proteins.
It is a simple pulling simulation. It is giving me the following error
ERROR 1 [file md_pull.mdp]:
When the maximum distance from a pull group reference atom to other atoms
in the group is larger than 0.5
Hi Users.
I have done a protein-ligand simulation in POPC bilayer using charmm ff for
1000ns. I want to calculate the osmotic pressure as well as the lateral
pressure of the system. Is it possible to do post simulation?
Lateral pressure calculation like i want to slice the box and get the
Dear users,Does anybody know a reliable, correct, tested version of
gromacs, that can be installed on high performance computing (HPC)
facility.Recently, I and my colleague performed the same simulation with the
same files but with different gromacs version, one
Dear all,
I am quite new to free energy calculation, so I apologize if the questions
seem naive and of course they are a lot.
My intention is to turn off vdw and coulombic interactions to perform some
tempering cycles on my system. There are though some questions:
1- I only want to
Hi,
The surface tension computed in gromacs is the integral of the difference
of the normal (Pzz) and lateral ((Pxx_Pyy)/2) pressure components along
direction z. This gives you 0 in an isotropic bulk but something positive
at the interface.
The surface tension is basically the surface free
Dear all,
I've a question. I've a PVDF polymeric membranes, for which I'd like to
calculate its surface tension. I performed a MD simulation of
crystallization and I'd like to know if it's possible if there's a method
to evaluate surface energy.
With command gmx energy, there's the possibility
Dear all,
I've a question. I've a PVDF polymeric membranes, for which I'd like to
calculate its surface tension. I performed a MD simulation of
crystallization and I'd like to know if it's possible if there's a method
to evaluate surface energy.
With command gmx energy, there's the possibility to
Hi GROMACS users,
I just released another patch release of GROMACS 2018, bringing the
official version to 2018.6!
We decided to release this additional patch due to issues found in
2018.5 that could affect scientific correctness, so we encourage all
users of the 2018
series to update to
