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Dear all, I want to distance restrain for an ion and its associated residue. There are 5 polymer chain and 200 ions( 40 for each chain). I made restrain.itp for my desire atoms and their...
11 August 2020 4,611 1 View
Dear researchers, I want to simulate a polymer at micro molar concentration in GROMACS. Whenever I try with simulation box of about 30 nm each side , the force is not converging. Therefore, if I...
02 August 2020 3,390 3 View
I have performed MD simulation to a trans membrane protein using gromacs 2018. Can anyone provide me way to calculate the tilt angle of the protein relative to bilayer? Also how can I calculate...
17 July 2020 8,090 1 View
Dear Researchers, I am quite new at using Gromacs, and trying to add H to my .PDB file using Gromacs. Though i added H using Maestro in my PDB file, gromacs gives error like 'Atom XXX in resiude...
15 July 2020 1,507 3 View
Hello, I've made an octane slab and would like to place a protein in it using lambada. Usually I use a membrane and then place the protein in it, and lambada has always worked. Now, it gives me...
15 July 2020 9,105 0 View
Dear researchers, please i used MD simulation for the complexe protein-ligand using gromacs software. but in equilibration phase i put this commands: gmx mdrun -deffnm nvt nsteps = 50000 and...
11 July 2020 2,737 0 View
Hi all, I'm trying to plot Free Energy Landscapes from Gromacs after using the gmx sham function. After using the command: gmx sham -f PCAplot2d.xvg -notime -ls gibbs1-2.xpm (where...
08 July 2020 1,245 1 View
It seems that polarization has been implemented in the Gromacs version of 2019 and further. However, I can't seem to find relevant info in the documentation except for the edits that have to be...
01 July 2020 1,989 3 View
Hi all, I had simulate charged polymers and surfaces, and is very common to have interaction of ion bridge (or ionic crosslinking) which consist of and interaction of two equally charged groups...
25 June 2020 1,755 1 View
I want to simulate polyelectrolyte of PPO . I inserted counterions into the simulation box and changed their position near the protonated group with position.dat file. but after minimization and...
20 May 2020 5,578 4 View
I am currently using gromacs 2020 for my MD simulation (Protein-Ligand) and i have g_MMPBSA 5.1.x installed. after entering the command, g_mmpbsa -f md_0_10_center.xtc -s md_0_10.tpr -n index.ndx...
06 May 2020 4,105 5 View
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 8,796 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 1,796 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 1,644 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 1,647 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 3,799 4 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 3,515 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 306 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 3,771 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 1,343 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 6,802 5 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 9,684 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 9,887 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 2,835 5 View