Amr Abbas

3 Questions 2 Answers 0 Followers

Questions related from Amr Abbas

How to generate multiple independent trajectories of the same system in Amber?

I am planning to run GaMD simulation in amber, and I want to produce multiple trajectories of the same system to run independent simulations of the system with different initial velocities. The...

30 May 2023 7,416 1 View

How to simulate Multiple Identical Chains in Gromacs?

I want to build a system of multiple, identical peptides, I saw other users suggest this documentation link http://www.gromacs.org/Documentation/How-tos/Multiple_Chains#Identical_chains However,...

12 November 2022 8,395 3 View

How to prepare a protein in case of targeting a newly identified pocket in Maestro Schrodinger

In case of having a newly identified pocket that might be druggable, and want to test it for docking, how can I prepare the protein in that case to avoid removing water molecules that might be...

01 January 1970 412 4 View