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Questions related from Laura Pulido
Hi everyone. I want to analyze the hydrogen bonds between dppc carbonyl oxygen O22 and cholesterol hydroxyl group O3 H3. However, when I execute the gmx hbond command, it doesn't find the donor...
06 May 2020 3,385 3 View
I want to calculate the rdf between O3 atoms of different cholesterol molecules. Additionally, I want to avoid the calculation of rdf between the same molecule. How can I do this in gromacs ?
01 May 2020 5,150 3 View
I'm using gromacs to simulate a lipid bilayer by MD and I'm using tip3 as water model. How can I calculate the volume per water molecule ? Thank you in advance.
03 April 2020 3,783 1 View
Hi everyone, I want to change the segid name of topology(in pdb format) and gromacs trajectory. To later generate a new topology and trajectory with the changed names. Do you know a way to do...
17 February 2020 2,998 1 View
Hi everyone, I have a lipid bilayer system of 100 DPPE lipid molecules per leaflet. I want to insert 100Na ions and 100 CL ions per leaflet. The system has the following dimensions in nm: 7.68 x,...
24 January 2020 4,698 0 View
Hi all, Could someone tell me how to calculate the electrostatic potential across the z axis of a lipid bilayer ? Also, I would like to calculate the potential from the lipid headgroup to a...
05 January 2020 3,398 9 View
Hello all, When I draw a lipid molecule in AVOGADRO from the smiles files obtained from Pubchem, I don't get the correct orientation and chirality of all atoms, How can I achieve this? Thanks in...
09 December 2019 3,535 1 View
Hi everyone. I'm currently using RNAcentral for my research project, but I don't know how to get information from the databases included in RNAcentral by using relational databases. I know that...
01 January 1970 5,761 3 View
