Re: AMBER: results from TI

From: Holly Freedman <freedman.phys.ualberta.ca>
Date: Mon, 22 Oct 2007 13:03:20 -0600

Hi Thomas,

Thank you for taking the time to look at my input and for your suggestions. I will try changing the
ntf, but this shouldn't effect interaction with water that much should it? I have pasted below the
input files for the soft-core step. I looked at the trajectories and they seem OK. I don't have any
experimental data to compare to, unfortunately. The free energy curves look pretty smooth, the
charging ones are linear and the charging energies can pretty much be determined just from the
lamdba = 0.5 simulations.

I am thinking that I would be better off letting the perturbation be from OCH3 to OH, charges on and
off OH and OCH3, rather than on and off H and CH3 and changing CH3 to H. This should work
better because in this case the molecule won't gain too large a charge when the partial atomic
charges are turned off since the OCH3 and OH groups should be closer to neutral than CH3 and H
(the overall charges of the molecules are all neutral). In this case I shouldn't have to use a noshake
mask at all, should I ? What do you think about this plan?

Thanks,
Holly

--
Department of Physics, University of Alberta
Edmonton CANADA
Files for perturbation in water:
 &cntrl
  imin   =    0,
  ntx    =    5, irest =     1, ntr = 0, iwrap=1,
  ntpr   =  100, ntwr  =   100, ntwx =  5000, ntwe = 5000,
  ntf    =    2, ntb   =     2, cut  =   10,
  nstlim = 500000, dt   =   .002, ntc  =    2,
  tempi  = 298.0, temp0 = 298.0, ntt  =    3, gamma_ln = 2,
  tautp  =  1.0, ntp   =     1,
  icfe = 1, clambda  = 0.01592, klambda = 1,
  ifsc = 1, crgmask = ':1.H10', 
  scmask = ':1.H10', noshakemask = ':1.H10',
 &end
 &cntrl
  imin   =    0,
  ntx    =    5, irest =     1, ntr = 0, iwrap=1,
  ntpr   =  100, ntwr  =   100, ntwx =  5000, ntwe = 5000,
  ntf    =    2, ntb   =     2, cut  =   10,
  nstlim = 500000, dt   =   .002, ntc  =    2,
  tempi  = 298.0, temp0 = 298.0, ntt  =    3, gamma_ln = 2,
  tautp  =  1.0, ntp   =     1,
  icfe = 1, clambda  = 0.01592, klambda = 1,
  ifsc = 1, crgmask = ':1.C3,H10,H11,H12', 
  scmask = ':1.C3,H10,H11,H12', noshakemask = '',
 &end
Files for perturbation in the vacuum:
 &cntrl
  imin   =    0,
  ntx    =    5, irest =     1, ntr = 0, iwrap=0,
  ntpr   =  100, ntwr  =   100, ntwx =  5000, ntwe = 5000,
  ntf    =    2, ntb   =     0, cut  =   10,
  nstlim = 100000, dt   =   .002, ntc  =    2,
  tempi  = 298.0, temp0 = 298.0, ntt  =    3, gamma_ln = 2,
  tautp  =  1.0, ntp   =     0,
  icfe = 1, clambda  = 0.01592, klambda = 1,
  ifsc = 1, crgmask = ':1.H10', 
  scmask = ':1.H10', noshakemask = ':1.H10',
 &end
 &cntrl
  imin   =    0,
  ntx    =    5, irest =     1, ntr = 0, iwrap=0,
  ntpr   =  100, ntwr  =   100, ntwx =  5000, ntwe = 5000,
  ntf    =    2, ntb   =     0, cut  =   10,
  nstlim = 100000, dt   =   .002, ntc  =    2,
  tempi  = 298.0, temp0 = 298.0, ntt  =    3, gamma_ln = 2,
  tautp  =  1.0, ntp   =     0,
  icfe = 1, clambda  = 0.01592, klambda = 1,
  ifsc = 1, crgmask = ':1.C3,H10,H11,H12', 
  scmask = ':1.C3,H10,H11,H12', noshakemask = '',
 &end
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Received on Wed Oct 24 2007 - 06:07:35 PDT