Questions tagged [molecular-dynamics]

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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 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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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 ...