Jakub Hryc

15 Questions 1 Answers 0 Followers

Questions related from Jakub Hryc

How can I learn parametrization by myself in molecular modelling?

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...

03 March 2020 9,000 1 View

How to calculate in GROMACS number of water molecules which create hbonds per lipid and water bridges?

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...

12 December 2019 4,227 2 View

Is there any program to create cylinder structure (molecular modelling)?

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...

09 September 2019 5,137 3 View

How to solve the problem with checkpoints in gromacs (managing long simulation with changing mdp options)??

I want to extend my simulation. I use Gromacs 2018.4. At the beginning (20ns) I use Berendsen thermostat and barostat and then (80ns) I change mdp file and use Nose-Hoover thermostat and...

06 June 2019 4,989 1 View

How to interprate this .mdp options?

I have a problem with interpretation of this mdp options. title = MD equilibration; dt = 0.002 ; 1 fs nsteps = 5000000 ; 10 000...

04 April 2019 9,452 0 View

How to center my membrane after simulation?

I ask you for help. I hope you will help me. I created my DOPC membrane I have a question. I try to center my membrane after production (md_0_1.gro). I try to use gmx trjconv -s md_0_1.tpr -f...

02 February 2019 9,980 1 View

Which .mdp files for equilibration for DGDG lipid bilayer?

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...

01 January 2019 5,608 2 View

How properly minimize and equilibrate my DGDG molecule (warnings and notes)?

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...

01 January 2019 4,747 0 View

How to make properly energy minimization of lipid bilayer?

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 5,811 3 View

How to build topology for the whole DGDG membrane?

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...

11 November 2018 10,106 1 View

How to add residue to topology database?

I have this error: "Fatal error: Residue 'UNK' not found in residue topology database" My residue UNK is Digalactosylodiacylglicerol. I use OPLS-AA force field. I created topology of my residue by...

11 November 2018 5,949 5 View

Any advice about angles in Pymol and dgdg 3d structure?

Do you know how to change angles in Pymol builder between atoms and where can I find 3d structures of lipids like dgdg (Digalactosyldiacylglycerol) or others lipids?

10 October 2018 2,384 1 View

How to properly place single lipid in xyz coordinate system to later construct whole bilayer?

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...

10 October 2018 5,005 2 View

Creating lipid bilayer - when energy minimization?

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...

10 October 2018 7,892 3 View

How to compare dihedral from articles and from topology in Gromacs?

I have a question. In the article I found description like that: OPLS-AA Torsional Parameters ( kcal / mol ) for Carbohydrates. Type V 1 V 2 V 3 H-C-C-H 0.0 0.0 0.318 H-C-C-C 0.0 0.0 0.366 And...

01 January 1970 1,391 2 View