Re: [AMBER] Ref Flag for Minimization

From: He, Amy via AMBER <amber.ambermd.org>
Date: Tue, 9 Apr 2024 22:14:39 +0000

Hi Will,

I did the same thing before. But I don’t think the previous restraints can be read from a refc file. With an existing refc file but no restraint specifications, my md output says:

Frozen or restrained atoms:
ibelly = 0, ntr = 0

and in the results session I always got:

RESTRAINT = 0.0000

Can you explain the differences you saw?

The few steps at the beginning could have exactly the same energies (and perhaps very similar structures). As the minimization progresses, the structures may start to diverge. However, the endpoint energies and structures should be relatively similar. You can check for RMSD per residue - comparing both min2.rst to min1.rst, and the two min2.rst to each other. Overall I think the difference with or without a refc in my system is very minor (the difference between two min2.rst is much less than their difference from my min1.rst). let me know what you think!


Best regards,
Amy 

--
Amy He
Hadad Lab @ OSU
He.1768.osu.edu
From: William Livernois via AMBER <amber.ambermd.org>
Date: Friday, April 5, 2024 at 7:48 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Ref Flag for Minimization
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 Tue Apr 09 2024 - 15:30:02 PDT
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