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Questions related to Gromacs
Hi all I am new to GROMACS and need help with some issues. (1) I am trying to run a simulation for glucose in water. The topology file for glucose was generated using AMBER and GLYCAM_06j-1...
05 May 2020 8,841 2 View
Is it valid to compare the wild type protein against the protein that has been truncated due to stop codon mutation using molecular dynamics simulations?
04 May 2020 1,833 3 View
Dear Gromacs users I am facing a problem between different versions of gromacs for gmx pdb2gmx. I have a protein-ligand system, I did all the necessary steps mentioned in gromacs manual for...
28 April 2020 1,705 3 View
Hi all, I am a newbie in the field of classical MD calculations for biomolecules, and I am running a few calculations for studying protein-ligand interactions using the GROMOS force field in...
28 April 2020 1,664 0 View
I would need to check the distance between the two centers of mass of a Protein and of an organic Ligand (the resname and the resnumber of the ligand are both known), inside a system containing...
23 April 2020 3,842 4 View
I have tried the electrochemical impedance spectroscopy (EIS) for a series of electrode materials in two different electrolyte solutions but surprisingly I came up with two completely different...
21 April 2020 6,602 0 View
I want to run an MD simulation using gromacs for metal ion bound protein. I need to know the parameters as well as the force-field used for this kind of simulation.
18 April 2020 3,535 1 View
Hello everybody, I'm trying to analyse secondary structure of a protein with do_dssp included in the program gromacs. My trajectories are of 200 ns each. when I run gmx do_dssp, it takes very long...
04 April 2020 327 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 3,797 1 View
Currently I use Gromacs to perform molecular dynamics of tobermorite 11A, but it turns out that this structure has a monoclinic box, I need to solvate my structure only above in the z axis, but I...
27 March 2020 1,384 3 View
I have performed simulation for Protein-Ligand complex in Gromacs. While in system preparation I have given: gmx editconf -f complex.gro -o newbox.gro -bt cubic -d 2.0 -c and ran simulation for...
26 March 2020 6,819 5 View
Dear all, Hi. I would like to do simulation for my full protein model (including transmembrane domain) extracted from Cryo-EM reported pdb file. I have used Orientations of Proteins in Membranes...
26 March 2020 8,618 0 View
Hi everyone. I have a trajectory that was calculated by Gromacs. 1) How can I calculate an h-bond lifetime between two selected amino acids (for example Arg32 (from A chain) and Glu 21 (from B...
23 March 2020 9,709 3 View
I have installed the ubuntu and Gromacs. I also installed the VMD. It says VMd installation is complete. Enjoy! But I cannot open the VMD window! When I try to open vmd, I get all these notes but...
21 March 2020 9,929 4 View
Greeting to all, I have modelled two different domains of the same protein from two different tools (example - 1-250 using ab initio and 250-400 a.a using modeller). Now to make it a full length...
17 March 2020 2,853 5 View
1. I am processing my umbrella sampling simulations using the Weighted Histogram Analysis Method in Gromacs (gmx wham). However, I would like to report the mean dG and a standard deviation. To do...
16 March 2020 1,605 3 View
Hi, I am familiar with performing MD simulations using Gromacs on protein-ligand complexes. However, BAR is a new technique to me and I need specific clarification of the decoupling sequence...
13 March 2020 3,764 1 View
I know that the change from Gromacs 4 to 5 changed quite a few things, but I believe gromacs is set up to be backwards compatible am afraid that I do not know what the settings that would need to...
11 March 2020 3,808 2 View
I am trying to simulation protein in non-aqueous solvents and I put my protein in MeOH with Charmm36 force field. After I tried to minimize the energy. it gives: Energy minimization has stopped,...
07 March 2020 8,360 3 View
Can anyone tell me how to estimate the turning movements at roundabouts with only counting the entry volumes at each approach? A generalizes equation or model to do that, or a prepared spreadsheet.
01 March 2020 5,225 0 View
Hello everyone, I have to do molecular dynamics of a metalloprotein. I have read in literature that we can use the CHARMM force field in Gromacs for metal protein. Beside CHARMM I also use...
28 February 2020 9,920 6 View
Hello everyone, I'm new to gromacs and also new to umbrella sampling, so I'm following Justin's tutorial http://www.mdtutorials.com/gmx/umbrella/index.html ; On the umbrella sampling stage, I'm...
21 February 2020 1,886 3 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 3,012 1 View
I want to know how to fix the separation of 2 chains after the production run. I'm trying different combinations of trajconv after creating an index file having a specific residue(s) on the...
13 February 2020 1,934 2 View