Hi Ross,
I see. Thank you for highlighting this to me. My previous simulation was
using CHARMM force field. I used the pmemd compiled by another person, and
it was named as amber11. Now I was not sure how it worked. I will be more
careful about the settings in future.
Best,
Mo
On Thu, Oct 13, 2011 at 3:59 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> > taup = 2.0,scee = 1.0,scnb = 1.0,
>
> Besides the fact that this has been removed from AMBER 11 - which force
> field are you using for your simulations here? I assume you were using
> these
> settings with earlier versions of AMBER where the scee and scnb scaling
> would have been applied. Note ONLY the GLYCAM force field should use
> non-default values.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Thu Oct 13 2011 - 13:30:02 PDT
