Lukasz Rzeznik

5 Questions 12 Answers 0 Followers

Questions related from Lukasz Rzeznik

Periodic boundary conditions in Gromacs 3.3.1 - molecules outside the simulation box. Is it ok?

Hello! I have to use some older version of Gromacs (3.3.1 which is installed on the cluster I used for run simulations). When I applied pbc (pbc=xyz in mdp file) I noticed that the output .gro...

04 April 2015 4,137 4 View

What Gromacs Force Field is able to model polystyrene molecules?

I was trying Oplsaa, which worked fine for me for polyethelene. But in the case of PS I had problems because grompp produced many warnings the same type: "No default Angle types, using zeroes"....

04 April 2015 5,583 5 View

Which free software can I use to generate amorphous polystyrene (PS) sample of certain density?

Till now I am using Polymer Modeller from nanohub.org. I works fine for polyethelene samples. But I noticed that for PS it sometimes produces "bad" molecules (open phenyl ring or some bonds to...

04 April 2015 9,223 12 View

Is the following procedure appropriate for creating amorphous polymer sample in Gromacs?

Let assume that I would like to create amorphopus polymer sample composed of C32H66 (dotriacontane) chains. I am trying to do it in the following way: 1. Create a single molecule (e.g. in...

02 February 2015 6,825 2 View

What is the minimum input file for performing organic molecule (e.g. butane) energy minimisation in Gaussian?

I am looking for rotational barriers (and shapes of energy vs dihedral angle) for a series of organic molecules having single, double and triple C-C middle bond (ethane, ethene, ethyne, propane,...

08 August 2014 447 0 View