AMBER Archive (2004)

Subject: Re: AMBER: target rmsd

From: Carlos Simmerling (
Date: Mon Sep 13 2004 - 15:49:30 CDT


it doesn't look like you set nmropt=1 to read the weight changes.
does the sander output actually list the changing target under "Begin
reading energy term weight
changes"? does that echo what you told it to do?

take a look at the test case for changing target,
that should be a good template for the correct format.

even if you resolve that, it might be hard to get from 2.0A to 0.5
directly without getting stuck.
to verify that it's working you might try going the other way first,
from 0.5 to 2A
since that should be easier. also see if the restraint energy is going up
as you reduce the target, since the force from the tgtmd might not be
enough to
overcome something that's keeping the system from reducing the rmsd
(such as
a side chain trapped somewhere, etc).


Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

William Andrew McLaughlin wrote:

>To anyone who may be helpful:
>I am trying to use targetted rmsd function for a molecular dynamics
>simulation. I would like to vary the rmsd level of the protein backbone
>during the simulation and have tried to use the weight function. My
>molecular dynamics input file is shown below. As you can see I am trying
>to vary the target rmsd from 2 anstroms (value1) down to 0.5 angstroms
>(value2). When I run the simulation it appears that the rmsd value does
>not vary and just stays at the second value of 0.5 angstrom rmsd. Any
>ideas on how to vary the target rmsd for the backbone during the
>simulation would be helpful.
>Bill McLaughlin
>short molecular dynamics simulation
> imin = 0, ntb = 0,
> igb = 0, ntpr = 100, ntwx = 100,
> ntt = 3, gamma_ln = 1.0,
> tempi = 300.0, temp0 = 300.0
> nstlim = 100000, dt = 0.001, nscm=1,
> cut = 999,
> ntr=1,
> restraint_wt=1.0,
> restraintmask=':2',
> tgtrmsmask='@CA,C,O,N,H',
> tgtmdfrc=1,
> tgtrmsd=0.6,
> &wt type='TGTRMSD',istep1=0,istep2=100000,value1=2.0, value2=0.5,
> &wt type='END',
> &end,
>William McLaughlin, Ph.D.
>Dept. of Chemistry and Biochemistry
>9500 Gilman Drive
>4th Floor Urey Hall
>La Jolla, California 92093-0359
>Phone: (858) 822-4240
>Fax: (858) 534-7042
>The AMBER Mail Reflector
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