Dear gromacs members,
I would ask you if in gromacs is possible to add a control parameter on the
Lennard-Jones interactions.
For example we have two atoms A and B and the corresponding parameters;
sigma(A), eps(A), sigma(B), esp(B); then for the A-B interactions we have the
parameters
Yes, the 36m (CHARMM36m) is the new set of parameters recommended by the
authors, so it is best to stick to the recommendation unless you know
exactly what you are doing.
Huang, J. et al., 2016. CHARMM36m: an improved force field for folded and
intrinsically disordered proteins. *Nature Methods*,
Dear Gromacs users,
I am trying to use the charmm36m forcefield to simulate a protein. The most
recent release of charmm36 includes 36m and the ability to toggle between the
two. Is 36m the default state?
Best regards,
Coire
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On 5/15/19 11:03 AM, ABEL Stephane wrote:
Hello all,
I am currently doing simulations of a model of membranes with different types
of lipids (LIPIDA, LIPIDB and LIPIDC) and I would like to select a group of
atoms for only the same lipid with make_ndx. Below an example
Three different
Hello all,
I am currently doing simulations of a model of membranes with different types
of lipids (LIPIDA, LIPIDB and LIPIDC) and I would like to select a group of
atoms for only the same lipid with make_ndx. Below an example
Three different lipids : LIPIDA, LIPIDB and LIPIDC contain few
Dear all,
The gmx dielectric command gives negative value of imaginary
part in gromacs-2018.3. I can't get the reason.
It will be highly helpful if someone make a suggestion.
Thank you.
Dhrubajyoti Maji
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Den 2019-05-15 kl. 08:12, skrev Harutyun Sahakyan:
Dear GMX users
I would like to use Young and Cheatham ions parameters (
https://pubs.acs.org/doi/full/10.1021/jp8001614#si1) with amber99sb-ildn.
How can I convert sigma and epsilon values and use them with gromacs? For
instance, I want to use
Dear GMX users
I would like to use Young and Cheatham ions parameters (
https://pubs.acs.org/doi/full/10.1021/jp8001614#si1) with amber99sb-ildn.
How can I convert sigma and epsilon values and use them with gromacs? For
instance, I want to use K and Cl ions with scpe water, sigma (*R* min/2)
and
