Dr Steinbrecher,
When I observed the dV/dL averages for 500ps for lambda = 0.99, the
restraint energy is -177.4749 kcal/mol which is the almost all the dV/dL
for my system.
The reason I had the restraints was to make sure that the K+ and Cl- dont
come close during the dual mutation.
Is there a better way to approach this?
Thanks for your help and time.
Regards
Sai
On Wed, Jan 18, 2012 at 12:54 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > V0:
> > restraintmask = ':1-2'
>
> > For V1:
>
> you are not only removing the salt from water, you are also restraining it
> in V0 only. This explains the dvdl behaviour that you see. Are you sure
> this is what you want to be doing? Your restraints have to be accounted
> for correctly in whatever thermodynamic cycle you are using.
>
> 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 Wed Jan 18 2012 - 11:30:02 PST
