Dr Steinbrecher,
If I have to manually remove or subtract the restraint contribution from
the DVDL,
should I use the values printed at the end of the simulation that reads:
DV/DL, AVERAGES OVER 500000 STEPS
Thank you for your time.
Regards
Sai
On Thu, Jan 26, 2012 at 9:39 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > But when the output file is generated by sander, in the section that says
> > Free energy parameters, I dont see dvdl_norest being printed at all.
>
> This print statement seems to be missing. The option should nevertheless
> be set correctly...
>
> > The input file for the V0 state:
> > ifsc=1, dvdl_norest = 1,
>
> > The mdin file for production run for state V1:
> > ifsc=1, dvdl_norest = 1,
>
> hm, this will not work. The manual should be clearer on that, but
> dvdl_norest is set up to work for restraints on the disappearing side
> only, not the appearing. This is because it is used for absolute binding
> free energies. It never occured to me that someone would like to remove
> and introduce restraint particles at the same time.
>
> However, you can just not use dvdl_norest and subtract the restraint
> contribution by hand.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Mon Jan 30 2012 - 14:30:02 PST
