17 Questions 1 Answers 0 Followers
Questions related from Jakub Hryc
I have a huge problem. I have a pdb which consists of 11 states. I try to select molecules from the first state and observe how they move in the next nanoseconds. When I have only pdb with one...
09 May 2022 3,099 0 View
I want to parameterize a few molecules. I need of course torsional, dihedral angles, charges , etc. What is the most popular program for that right now? I know that gaussian is quite popular, but...
02 August 2021 176 2 View
I want to measure water flux across the membrane. This water flux is described here: https://pubs.acs.org/doi/10.1021/acs.jpcb.6b01870 "Water flux across the membrane Based on the number of...
12 February 2021 6,984 0 View
GROMACS version: 2018.4 GROMACS modification: No I have a question. I want to know one thing. How is computing autocorrelation function, because I am not sure about something. I try to calculate...
08 February 2021 9,691 1 View
I have a question. I want to measure the volume per lipid. I built a membrane with water and run the simulation for 300 ns. To measure the volume per lipid I used a .gro file from the simulation...
23 October 2020 2,463 3 View
In gromacs gmx order computes the order parameter per atom for carbon tails. For atom i the vector i-1, i+1 is used together with an axis. then we use this S mol = 1/2(3cos^2 (θ ) − 1),. So to...
02 August 2020 5,928 2 View
I want to create MGDG (monogalactosyldiacylglycerol) reversed hexagonal phase, but I have a problem. I constructed a system that consists of two bilayers and an inner water layer between these two...
05 May 2020 7,805 0 View
Is it possible to learn parametrization by myself? Do you know some good books, videos about that? I found that https://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf but I...
02 March 2020 8,827 4 View
I created a MGDG membrane I want to know how can I calculate number of water molecules which create hydrogen bond with lipids per lipid. Gromacs can only calculate number of all hbonds between two...
05 December 2019 9,139 2 View
I saw that in Packmol I can create initial configuration for bilayers and spherical structures, but is it possible to create cylinder structures? I want to create reversed hexagonal phase (HII in...
30 September 2019 1,191 3 View
I have a problem. I have this warning when I minimized my DGDG membrane. NOTE 1 [file step6.1_equilibration.mdp]: The Berendsen thermostat does not generate the correct kinetic energy...
17 January 2019 6,800 0 View
I have a question. I created DGDG (Digalactosyldiacylglycerol) membrane from scratch. I created DGDG molecule in Pymol. Then I rotated this molecule to have my acyl chain along z-axis. Then I...
07 January 2019 4,898 2 View
I created DGDG (Digalactosyldiacylglycerol) membrane from scratch. I created DGDG molecule in Pymol. Then I rotate this molecule to have my acyl chain along z-axis. Then I created 8x8 down layer...
12 December 2018 6,124 2 View
How to build topology for the whole DGDG membrane? I created DGDG (Digalactosyldiacylglycerol) membrane from scratch. I created DGDG molecule in Pymol. Then I rotate this molecule to have my acyl...
19 November 2018 8,395 2 View
I want to ask about energy minimization. I want to create DGDG lipid bilayer, which is consist of 128 DGDG molecules (64 per layer). So I created a molecule in Pymol. Should I try to do energy...
25 October 2018 3,019 2 View
I created a single DGDG molecule (digalactosyldiacylglycerol) in Pymol. The next step is: Once structure of first molecule is prepared, it must be aligned so that its main axis is parallel to the...
08 October 2018 2,998 2 View
I read that in order to facilitate the production of huge amounts of membrane for oxygenic photosynthesis, that is, taking place with the release of oxygen (as opposed to anoxygenic...
01 January 1970 2,012 1 View
