[AMBER] Use amber output velocity for different system

From: Khabiri, Morteza <khabiri.med.umich.edu>
Date: Mon, 29 Jan 2018 16:48:11 +0000


I have an equilibrated DNA system. I have generated a point mutation in my equilibrated DNA system and want to run mutant DNA for sometimes. However, except for the atoms in mutated nucleotide(nt), I want to use the velocity from my output wildtype DNA system (restartfile) as an initial velocity for the rest of the atoms in my mutated DNA system. For the atoms in mutated nt, I am going to generate velocity based on maxwell-Bultmann distribution. Is there any way that I can extract the velocity for all atoms except perturbed one from wildtype system, and use it as an initial velocity for the atoms in mutated system?


Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
AMBER mailing list
Received on Mon Jan 29 2018 - 09:00:03 PST
Custom Search