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Questions related to Gromacs
When I calculate the order parameter for lipid molecules I get positive value but many papers reports -SCH value. So is gromacs reporting -SCH values?
15 March 2021 773 8 View
Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...
04 March 2021 10,697 2 View
I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...
26 February 2021 7,069 1 View
I have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.
19 February 2021 5,195 2 View
I am trying to calculate the rdf of water molecules present inside the Carbon nanotube. I tried to do the indexing first using gromacs tool gmx selection. But when it comes to calculating rdf, I...
18 February 2021 1,559 3 View
Good day everyone! I am a Biochemistry undergraduate in the Philippines and to be very honest, we have no background in bioinformatics since we really focused on wet lab techniques + theory. Due...
16 February 2021 3,925 4 View
Dear All, I received a comment from reviewer about asking me selection of force field and water model. I choose OPLS-AAL and 3-point water model. They mentioned the combination of OPLS-AAL and SPC...
14 February 2021 1,831 3 View
I need to estimate the mobility of some atoms in the molecule within a molecular dynamics simulation and compare the values for different simulations. I use trjconv -fit rot+trans to fit C-alpha...
20 January 2021 785 3 View
The ligand.str file generated using cgenff is only compatible with charmm36. Any suggestions on how i can convert this str file into the gromacs topology file using Charmm27 ff?
08 January 2021 8,893 1 View
Hi, I got the following error message while running parallelized simulations with OpenMP: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off...
03 January 2021 4,968 5 View
"Steepest Descents converged to machine precision in ,5780 steps but did not reach the requested Fmax
27 December 2020 1,538 3 View
Hello all, I want to do glycosaminoglycan (GAG) simulation in Gromacs. Initial structure and CHARMM topology for short chains can be obtained from Charmm GUI glycan modeler. But I have to take...
24 December 2020 6,405 2 View
Hello, I am using the one-step approach from https://rashmikumari.github.io/g_mmpbsa/single_protein_ligand_binding_energy.html to calculate binding energy between protein and ligand. However, I...
10 December 2020 7,508 1 View
Hi all. I have a query. It is about Whether GROMACS can do rmsd restraint of a protein throughout the whole simulation. I found Gromacs can do only position restraint. But my intention is the...
22 November 2020 684 4 View
Which one has the most proper search algorithm and accuracy of docking? Can the online docking servers a suitable substitution for docking software?
16 November 2020 659 4 View
I want to simulation cytochrome C that it has two parts HEME and protein. I have charmm files par_heme.pdf and top_heme.pdf heme group but I do not know how to convert pdf file to *. inp because...
14 November 2020 8,089 2 View
I tried to run a 500ns MD simulation of a protein in Gromacs. Due to power failure, my pc turned of after around 450+ ns. Now I want to restart the simulation from that point. I used the following...
14 November 2020 9,435 3 View
I am running MD simulations for holoenzyme in Gromacs. The protein has four chains like A, B, C, D. After MD simulations, All the chains are showing as X chain in VMD and even in the PDB file....
13 November 2020 6,454 1 View
I have done 100ns simulation using Gromacs. To calculate the RMSF, I used the following command- gmx rmsf -f md_noPBC.xtc -s md.tpr -o rmsf.xvg -res But when I plotted the graph in excel, I found...
13 November 2020 4,938 2 View
I'm currently running a protein simulation on GROMACS. I was originally using CHARMM22/CMAP for the simulation, but with some reasons I decided to switch to CHARMM36. The thing is, I expected...
11 November 2020 9,157 1 View
How can I calculate Hydrogen bond life time in Gromacs between two groups like water-water and water-specific group in a polymer?
11 November 2020 2,605 3 View
I am trying to use the gmx energy model to make free energy calculations upon binding of a ligand to a receptor. To do this I am invoking the energy module and adding the -odh flag: gmx energy -f...
10 November 2020 1,922 3 View
hi. I have done electrostatic potential analysis on a symmetric bilayer contains 10% Cholesterol but I've got this figure and I thought there is a problem with that as the potential is not...
10 November 2020 7,376 1 View
I have an enzyme, which has a small one turn alpha helix present on a loop surrounding the active site. I have to mutate one of the residues on the alpha helix with proline, so that it may be a...
04 November 2020 2,126 2 View