AMBER Archive (2009)

Subject: Re: [AMBER] My step size

From: Vikas Sharma (
Date: Tue Apr 21 2009 - 23:49:47 CDT

Hi Ross,
Thanks for the reply...
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..
thank you

From: Ross Walker <>
To: AMBER Mailing List <>
Sent: Tuesday, 21 April, 2009 4:57:07 PM
Subject: RE: [AMBER] My step size

Hi Vikas,

Yes as long as you are always using shake (ntc=2) it should be okay to use a
2fs timestep for temperatures around 300K.

All the best

> -----Original Message-----
> From: [] On
> Behalf Of Vikas Sharma
> Sent: Monday, April 20, 2009 11:50 PM
> To: amber
> Subject: [AMBER] My step size
> Dear All,
>  I am working on MM PBSA..
> As per the tutorial I am minimizing,heating & equilibrating the protein
> -ligand complex...
> I used a step size of 0.001 ps for heating....
> will it be ok for me to use a step size of 0.002 ps for equilibration
> and production MD coz running with 0.001ps is taking a lot of time...
> I have applied SHAKE
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