Hi,
Thanks for response! Just to clarify tiny bit further-
The "RMS" value pointed to above is the root mean square of the elements
of the gradient, and indeed has units of kcal/mol*A.
Given the description in the manual as the DRMS being the RMS of the Cartesian elements of the gradient, I'm assuming that's from the new minimized function/previous function that the minimizer arrives at, and not tied to the system coordinates (ie, RMS from one step to the next minimized step)?
Best,
Kenneth
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Thursday, October 22, 2020 8:42 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] drms comparison in sander during minimization?
On Wed, Oct 21, 2020, Kenneth Huang wrote:
>
>A quick question- when we set drms=1E-4, what exactly is sander (or
>pmemd) comparing the value to in the output? Ie, given the final reported
>step from sander-
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 32599 -1.9473E+02 5.9628E-05 1.6881E-04 C2 20
>
> BOND = 0.5890 ANGLE = 4.4009 DIHED = 7.0049
> VDWAALS = -2.7607 EEL = 87.7876 EGB = -44.1792
> 1-4 VDW = 5.4083 1-4 EEL = -252.9773 RESTRAINT = 0.0000
>
>I'd been assuming it's the RMS value, but I realized the units don't
>quite make sense since drms is kcal/mol*A, whereas RMS should just be A
>unless it's not the strict Cartesian RMS that I've been thinking it was?
RMS means "root mean sqaure", and it doesn't per se specify what one is
taking the root mean square *of*.
The "RMS" value pointed to above is the root mean square of the elements
of the gradient, and indeed has units of kcal/mol*A. It should probably
have been labeled "DRMS" (derivative RMS) both for clarity and to match
the input variable drms.
....dac
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Received on Thu Oct 22 2020 - 21:00:02 PDT
