Gonzalo Quezada

6 Questions 7 Answers 0 Followers

Questions related from Gonzalo Quezada

How can I create a topology in Gromacs for a small alcohol molecule?

Greetings I'm trying to use the drude forcefield in gromacs for a small alcohol molecule.I tried to follow the topology of aminoacid as an example. I put drude particules in every Carbon atom and...

11 November 2018 4,089 0 View

How to obtain surface charge density from experimental data?

Greetings, I need the surface charge density of particulate solid at diferent pH. I have tried from the surface complexation model but there are several things missing. I only have the zeta...

09 September 2018 364 3 View

How to calculate water orientation for the SWM4-NDP water model in gromacs?

Hi I use the gromacs package (2016) for simulate polarized water and ions. When I try to use the h2order for water orientation I get wrong results (file attach). I use the make_ndx to create a...

07 July 2018 3,567 0 View

What basis is proper for aluminum oxide?

I use Gaussian to obtain the partial charges from a slab of aluminum oxide (corundum) with a hydroxide surface. the keywords that I use is # b3lyp/6-31+g(d,p) nosymm pop=npa geom=connectivity...

01 January 2017 8,644 4 View

Is it possible to use an OPLS potential in conjunction with other potentials originally created with an arithmetic mixing rule for sigma?

I'm using Gromacs 5.0.2 for a MD simulation with polymer in a saline solution, but the parameters for the polymers are not know, so I'm using OPLS, but this create a incompatibility with the other...

04 April 2016 9,321 4 View

How to rendering HQ images in VMD with polyhedra drawing method?

Hi I try to create an HQ image with VMD with the Tachyon option, but when I try to render an error message appear when the molecules are drawing with polyhedra...

01 January 1970 1,606 1 View