[25-VII-2013]
Hi everybody,
I am reading the subroutine runmd() in file runmd.f in amber11 code and I have found in the first Soft Core code in section "MAKE A FIRST DYNAMIC STEP" the next "if-statement":
if ( ifsc == 2)
! If this is a perturb to nothing run, scale forces and calculate dvdl
call sc_nomix_frc(f,nr3,ener)
...
end if
I have been reading amber11 manual and I have found that flag ifsc (in pg. 102) has only two possible values:
= 0 SC potentials are not used (Default)
= 1 SC potentials are used
but nothing about ifsc = 2.
I was wondering, what does it mean "a perturb to nothing"? Is that the case when you have a solute in a solvent box and you make it dissappear according to lambda to calculate the hydration free energies?
I run a hydration free energy calculation one month ago and I just selected the ifsc=1 flag with the appropriate topology and coordinate files for the starting and ending states. Is that right?
Thank you for your help!!
Kepa K.
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Received on Thu Jul 25 2013 - 09:30:03 PDT
