Hi Rahul,
I've run into a similar issue a year ago. It is possible to configure gmx
with the extra configuration file (as described in the documentation) to
get this right.
However, I found it to be archaic and wrote my own quick DSSP visualiser in
matplotlib.
I am planning to improve the code
On 3/16/19 9:06 AM, Mohsen Asadbegi wrote:
Thanks for your answer,
I want to simulate interaction of amyloid-beta peptide and CU(II) ion in
non-bonded modes. Non-bonded parameters of some metal ions like ZN(II),
CAD(II), and CA(II) are provided in CHARMM36. So what is the difference
among
Thanks for your answer,
I want to simulate interaction of amyloid-beta peptide and CU(II) ion in
non-bonded modes. Non-bonded parameters of some metal ions like ZN(II),
CAD(II), and CA(II) are provided in CHARMM36. So what is the difference
among copper ion and zinc/cadmium and calcium ions?
Hello,
Classical force fields are a bad way to describe the behaviour of
transition metals such as CU2+, because they are not able to cover the
behaviour of the D-orbitals with just the sigma and epsilon parameters.
What are you planning to use the model for? It is possible to parametrize
Dear Friends,
I performed REMD by following tutorial provided by Mark Abraham, But I
am not able to get the analysis part. Is a step-wise tutorial
available ? I would be thankful to you if anyone of you could help me
to perform analysis of REMD output. Thanking you
Regards
RajP
--
Gromacs Users
Dear all
I encountered with following error when running the umbrella sampling
simulation of a protein. What modification should I make in the pull code
to get rid of the error.
ERROR 1 [file npt_umbrella.mdp]:
When the maximum distance from a pull group reference atom to other atoms
in the
