AMBER Archive (2009)

Subject: [AMBER] help regarding step size

From: Vikas Sharma (
Date: Wed Apr 22 2009 - 03:57:31 CDT

hi all..
I am using MM PBSA..

the thing is that i first heated the protein for 50000 steps with 1 fs time step(50 ps total)
 coz when i used 25000 steps with 2fs time steps there was error regarding velocities...

so i used 50000 steps with 1fs time step for heating...then i equilibrated for double the no. of steps i.e. 100000(100ps total) in heating steps with 1fs time step...(hope this much equilibration would be ok as in tutorial its been asked to equilibrate fr 250 ps....)

now i want to run production MD for 1ns using 2fs time step..wont there be any problem coz i will be varying the step size from 1fs (during heating and equilibration) to 2fs during production MD..
thank you

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