Hi all,
I am working on minimization of DNA heterostructures with custom ligands
and I'm getting some strange results when I use the -refc flag (tested on
both sander and pmemd.mpi, Amber18). My understanding comes from the manual
which states:
refc input (optional) reference coords for position restraints; also used
> for targeted MD
>
This means that it should only be relevant for minimizations with
restraints, correct? Since we are doing a two step minimization, it makes
sense to use this flag for the first step:
Minimization of water molecules and counterions
&cntrl
imin=1, ! Energy minimization
maxcyc=5000, ncyc=250, ! Total of 5000 cycles; first 250 steepest
descent, then conjugate gradient
ntb=1, ntp=0, ! Constant volume
cut=10.0, ! Non-bonded cutoff
ntr=1, ! Apply restraints
restraintmask=':1-16', ! Restraints applied to residues 1 to 16
restraint_wt=50.0, ! Weight of the restraints
ioutfm=1, ntxo=2, ! Binary NetCDF output
&end
but not for the second step:
Minimization of the whole system
&cntrl
imin=1, ! Energy minimization
maxcyc=5000, ncyc=250, ! Total of 5000 cycles; first 250 steepest
descent, then conjugate gradient
ntb=1, ntp=0, ! Constant volume
cut=10.0, ! Non-bonded cutoff
ioutfm=1, ntxo=2, ! Binary NetCDF output
&end
However, when I accidentally used the -ref flag for the second minimization
step (*using the restart file from the first minimization step*) I got a
very different output result. Note nothing else was changed between these
results, using the same input files/force field/system setup. Does
including the ref flag change anything else about the forces or maybe keep
restraints used in a previous run?
Thanks,
Will
--
William Livernois
Dept. Electrical and Computer Engineering
Email: willll.uw.edu
Phone: 813-323-1920
Pronouns: he/him/his
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Received on Fri Apr 05 2024 - 17:00:02 PDT
