Hello,
I have two question regarding the simulation of a solute in different
lipid solvent (mixture of triglyceride, which is a simplified version of
the complex oil) as well as other solvents like carbitol.
I use the parameter from cGenFF together with the charmm36 forcefield.
First
On 11/8/18 10:58 AM, Farial Tavakoli wrote:
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
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
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
Paper explaining dispersion correct, and what it is:
http://dx.doi.org/10.1021/jp0735987
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
Dear gmx users
I am trying to simulate my complex using amber99sb ff. There is no amber
tutorial in gromacs. I need to know how dispersion correction set in the
.mdp files . I can not understand the definitions of DispCorr in mdp
option. Should I put it on EnerPres or no ?
Would you please
Hello,
I'm planning on studying several large protein clusters using the gromos
54A7 force field with the following cutoff parameters: rlist=1.0 nm,
rcoulomb=1.0 nm (long range handled by PME), rvdw=1.4 nm, and the short
range list will be updated every 10 steps. I am interested in studying
