AMBER Archive (2009)

Subject: RE: [AMBER] My step size

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Apr 21 2009 - 06:27:07 CDT

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
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] 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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