AMBER Archive (2009)

Subject: Re: [AMBER] help regarding step size

From: Vikas Sharma (
Date: Wed Apr 22 2009 - 05:50:27 CDT

Hi carlos...
thanks for the reply..
I first minimized the hydrogens and water, the minimized the whole system, then heated the sytem for 50 ps(50000 steps step size 1fs), then equilibrated for 100ps(1000000 steps,step size ifs)..
my questions are:
1. do i need to equilibrate more(the density has stabilized to 1.03 and temp has also stabilized around 300)
2. Now for production MD ca i change the step size from 1fs to 2 fs?

From: Carlos Simmerling <>
To: AMBER Mailing List <>
Sent: Wednesday, 22 April, 2009 3:43:54 PM
Subject: Re: [AMBER] help regarding step size

do you mean you did a single heating run and that's all for equilibration?
probably not nearly good enough. a good equilibration protocol should include
multiple steps, with slow turning off of restraints on various sections.
first equilibrate the solvent fully, along with H atoms and anything
else added. keep
what you know from expt restrained. minimize first, then do heating
MD. then, slowly turn
off restraints on side chains, since they can be involved in surface
packing or may otherwise need to move.
only then do you turn off restraints on the backbone. similar ideas
should be applied to non-protein.
also we use molprobity first to check for Asn/Gln flips in the initial
if you just build, head and go I'd expect some real problems even if
it doesn't crash.

On Wed, Apr 22, 2009 at 4:57 AM, Vikas Sharma
<> wrote:
> 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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