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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.

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Extract single frame with MDAnalysis

How can I do to extract a single frame as a pdb file from a trajectory traj.xtc file, by using MDAnalysis? I've got a universe u=mda.Universe('confout.gro','traj.xtc') Then I selected a residue by ...
Ivo Palabra's user avatar
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1 answer
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plot the relation between RMSD and free energy

how can i plot the relation between rmsd and free energy like the image i attached as i need to find the most stable conformation structure for my cycle peptide after finishing REMD simulation
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Generating intercalation site in DNA for custom sequence

Thank you for your help. Can anybody please tell me how I can generate an intercalation site in DNA at the base pairs I am interested on. I appreciate if you can please guide me to any tutorials or ...
dnalectronics's user avatar
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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 ...
miRastic's user avatar
1 vote
2 answers
644 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 ...
musako's user avatar
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3 votes
1 answer
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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 <...
musako's user avatar
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2 votes
1 answer
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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,<...
musako's user avatar
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1 vote
1 answer
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Nonbonded interactions on the GPU

i'm using this command gmx mdrun -deffnm nvt0 -nb gpu but got ...
user5520049's user avatar
1 vote
2 answers
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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 ...
user5520049's user avatar
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0 answers
513 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. ...
Camps's user avatar
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3 votes
1 answer
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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 ...
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