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!!
Regards,
Skanda
&cntrl
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
dt=0.001,
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,
gti_lam_sch=1,
${timask1}
${timask2}
${scmask1}
${scmask2}
clambda = 0.5,
/
&wt TYPE='END' /
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Received on Mon Feb 13 2023 - 00:00:02 PST
