Dear amber users,
I have looked into many tutorials but I am confused regarding few things
I know for before running molecular dynamics simulation
1) We need to solvate system
2) Add ions to make system neutral.
3) Minimize the water molecules and counter ions followed by minimizing entire system
Before heating up the system and equilibrating with protein restraints and finally proceeding for MD
Do we need to perform steps 1 to 3 before simulated annealing too?
Regards,
Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, 18 science drive 4, Singapore 117543, Republic of Singapore: sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ; Phone +6582969643; http://www.linkedin.com/in/imsharmanitin
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Received on Sun Apr 20 2014 - 07:00:02 PDT
