Questions tagged [gromacs]

GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Its command line interface and python API are designed to make simulations on such molecules easy to setup, run, and analyze.

Filter by
Sorted by
Tagged with
0
votes
1answer
20 views

GROMACS RMSF Result Analysis Problem

This is RMSF for protein from GROMACS after 100ns simulation- I have few questions- Residue numbers are starting from 1650 to 1850, has it ignore LIG and HOH as residues? There are three lines, so ...
1
vote
2answers
83 views

How to make a video of a gromacs gmx dump standard output with VMD

I did gmx trjconv on GROMACS trr file to generate a .xtc file, and then used ...
3
votes
1answer
40 views

GROMACS Coordinates and velocity and force trajectories do not match accuracy

I am using GROMACS to perform MD simulations of proteins. So, I tried to record the simulation results nstxout, nstvout, and <...
2
votes
1answer
31 views

What are the units for the force output by nstfout, the velocity output by nstvout, and the coordinates output by nstxout in gromacs?

What are the units of force, velocity, and coordinates output by gromacs trajectory? In .mdp, they are specified by nstfout,<...
0
votes
1answer
170 views

Nonbonded interactions on the GPU

i'm using this command gmx mdrun -deffnm nvt0 -nb gpu but got ...
1
vote
2answers
451 views

gmx mdrun error: "Error in user input: Invalid input values In option s"

I'm new to bioinformatics and gromacs I tried to run the code and got this error ...
0
votes
0answers
82 views

MM/PB(GB)SA calculations for DESMOND trajectories

I did molecular dynamic simulations with DESMOND. Now, I want to obtain the interaction free energy using MM/PB(GB)SA. The free tools I found to perform such calculations are AmberTools and g_mmpbsa. ...
3
votes
1answer
103 views

Gromacs molecular dynamic simulation throwing error during minimization

I am trying to investigate a membrane proteins influence on a lipid bilayer using molecular dynamics. I am new to MD and trying to run my first simulation. I have built the simulation input files ...