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Which is more appropriate for the binding energy? Neither.
Obi-Wan voice: "These are not the energies you're looking for."
If I understand your goal, you're trying to compare two ligands and determine which is better at binding to a given protein (and, ideally, quantify "how much better" one is compared to the other). If that is the case, ...
11
I'm not sure why you would use radius for gyration as a measure of solubility. Radius of gyration roughly measures how "unfolded" (or more accurately, how "stretched out") a polymer is. Although this may correspond to a higher solvent accessible surface area (which can itself be calculated and is useful in some cases), it has nothing to ...
8
Is there an option in gmx mdrun to specify where to write the .xtc file? For example I want to specify specific directory path with large disk space.
When you use the -deffnm md argument to gmx mdrun, it is assumed that all of the files will have the base name of md, so gromacs looks for md.tpr as input, and it writes md.xtc, md.edr etc. as output files in ...
8
You could use mol smoothrep x y z
where
x is the molid
y is the representation number (starts from 0)
z is the trajectory smoothining window size
In your case, for molid 0 and for protein representation and trajectory smoothing window size of 5, the command will be
mol smoothrep 0 0 5
and for representation of resname PEP, the command will be
mol smoothrep ...
7
You need the chemical potential to do solubility
The problem with solubility of large molecules, is that you need to know the chemical potential in the liquid and the solid. You can use Free Energy calculations to get the residual contribution to the chemical potential in the liquid, but, the residual contribution to the chemical potential of the solid is ...
7
How about this, also writes to a log file. This selects both group 1 and group 13 and write the indices to a index file (index.ndx)
echo -e "1|13\nq"| gmx make_ndx -f em.gro -o index.ndx|& tee -a youlogfile.log
7
Note: there's nothing specific to Gromacs in the answer below. These are just shell scripting techniques that are relevant to any program that takes input from stdin. For cases where I know that colleagues have needed this with Gromacs, we've used the first option listed below (heredoc). FWIW, I didn't test either of these with Gromacs, but they should work.
...
5
Just complementing the @dwhswenson answer, when studying ligand/protein binding process, there is no best energy to look for.
In the binding process there are several mechanism that will influence it. Knowing the influence of such and each mechanism, you can design your ligand accordingly to increase the binding.
One of the advantage of using force fields is ...
4
The cause to use restrains is due to a previous knowledge (i.e. experimental) of system behavior/characteristics that you want to include/retain/reproduce in your simulations.
In the case of protein-ligand complex simulations, they encode specifically prior knowledge about the macromolecular system to be simulated and is built of several components. These ...
4
Its neither a biophysical effect nor a bug in your MD simulation steps. It's just an visualisation issue. You could use the gmx trjconv command to make your protein and ligand to the center of the box and fit all atoms to a reference structure.
gmx trjconv -s yourTpr.tpr -f yourTrr.trr -pbc mol -center -o yourTrr_centered.trr
Clear details of individual ...
2
I got the answer to this question on the GROMACS forum which can be found here.
the thermostat influence in the non-equilibrium cosine perturbation approach is automatically taken care by GROMACS, which biases termperature rescaling based on the velocity profile of fluid particles.
However, some thermostats will introduce additional ‘artificial’ viscosity, ...
1
Check DFTB+ with its xtb implementation.
Among DFT codes working with ASE, take a look on GPAW, where you also have an external field option.
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