Questions tagged [molecular-dynamics]

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How to create an Alchem configuration file for NamD simulation?

I am trying to use NamD for Alchem simulation for a bilayer system. I am using the script below as the configuration file, but after the minimization step, I am getting this error: "FATAL ERROR: ...
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run NamD on Mac [closed]

I am trying to run NamD on mac, I changed the directory to the place the named file exists, but NamD still cannot be run. Does anyone help me with what script should I use in the terminal to run the ...
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Creating hybrid topology using VMD

I wanna create a Hybrid topology for alchemical free energy calculation. I am using the VMD plugin mutator to create that hybrid topology. But, I am facing this Error: unable to load structure file ...
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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 ...
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Drug-DNA complex simulation using AMBER

I want to carry out the simulation of drug-dna complex by placing the drug molecule at particular site in my DNA sequence (intercalating site). I have PDB files of both drug and DNA sequence. I will ...
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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 ...
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Sending chimera MD to remote computer

I am using Terminal to try to run Chimera MD simulations on a remote server/computer. I have been able to successfully connect using the command ssh username@detroit05 (and then entering the password)....
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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 ...
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Tutorial for DESMOND steered molecular dynamic simulation

I would like to perform a DESMOND steered molecular dynamic simulation. Til now, I found that I can use the biasing force plugin. Is there any tutorial about how to do this type of simulation?
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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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