[AMBER] scalpha and scbeta defaults are not right for TI calculations with smoothstep gti_lam_sch=1?

From: Skanda Sastry via AMBER <amber.ambermd.org>
Date: Sun, 12 Feb 2023 23:47:36 -0800

Hello all,

Thank you so much for all of your help. The mailing list archive is a great
place to come for help with alchemical calculations.

One thing I noticed after reading this paper (
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7494069/#SD1) and page 497 of
the Amber22 manual is that when the gti_lam_sch is set to 1 (lambda
scheduling), default scalpha is supposed to be 0.2 and default scbeta is
supposed to be 50. However, when I look at my resulting output file I see
that scalpha remains at 0.5 and scbeta remains at 12. When I run TI with a
charged amino acid this leads to a particle collapse problem.

Is there anything wrong I am doing? Here is an example script. The
timask/scmask are automatically filled in with a script. If there is
nothing wrong with my input script, is it possible for those defaults to be
changed so that it is in accordance with the manual? Thank you so much!!



  imin=0, !minimization off

  irest=1,ntx=5, !read coordinates,velocities

  ntpr=10000, !energy information in mdout

  ntwx=10000, !coordinates will be written to trajectory

  nstlim=5000000,!5ns equilibration run


  ntt=3, !langevin dynamics

  gamma_ln=1.0, !collison frequency

  ig=-1,!random number generator

  ntc=1, !no SHAKE

  ntf=1, !

  cut=8, !nonbonded cutoff

  ntb=1, !constant volume

  tempi=300.0, !initial temperature

  temp0=300.0, !final temperature

  iwrap=1, !coordinates written to the restart and trajectory files will be
"wrapped" into a primary box.

  ioutfm=1, !netcdf trajectory

  icfe = 1, ifsc = 1,






  clambda = 0.5,


 &wt TYPE='END' /
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Received on Mon Feb 13 2023 - 00:00:02 PST
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