Hello Danilo,
You can use positional restraints for this. In order to do that, add these flags into your mdin file:
ntr=1, ! Turn on positional restraints
restraintmask='.CA,C,O,N', ! restraints on the backbone atoms only
restraint_wt=10.0, ! 10.0 kcal/mol.A**2 restraint force constant
Add on your restraintmask flag the name of all atoms you want to restrain (on the example I am sending above there are typical names for backbone atoms). 10.0 at restraint_wt is a value people generally use during some minimizations, thus play with this value until you get the effect you want (in your case, higher values).
Don't forget to provide a reference structure for the positional restraints to pmemd or sander using the flag -ref . In your case, this structure would be the initial structure of your simulation.
I hope this helps,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: danilo gonzalez <dgnzlzf.gmail.com>
Sent: Friday, October 27, 2017 12:14:30 PM
To: amber.ambermd.org
Subject: [AMBER] frozen atoms.
Hi everyone,
I have some troubles to freeze some atoms during an MD calculation. The
system contains a protein and a water periodic box. In this calculation, i
want to freeze the protein residues and let the water residues to
redistribute.
I it try using the next input:
Solvent Equilibration
&cntrl
imin=0, ntx=5, irest=1,
ntb=2,cut=8.0,
ntp=1,
taup=2,
ntc=2,
ntf=2,
iwrap=1,
barostat=1,
ntt=1, temp0=300.0, gamma_ln=0.0,
nstlim=2500, dt=0.002,
ntpr=100,ntxo=1,ntwr=100,ntwx=100,ntr=1,ig=19,
nmropt=1,
/
&wt type='TEMP0', istep1=0, istep2=2500,value1=300.0, value2=300.0
/
&wt type='END'/
Protein fixed
10.0
RES 1 464
END
END
Increasing the value of the force constant I achieve to reduce the RMSD of
the system without making it 0.
I've also tried to do the same using the ibelly=1 parameter, but the
freezing is not successful.
Solvent Equilibration NPT 5 ps
&cntrl
imin=0, ntx=5, irest=1,
ntb=2,cut=8.0,
ntp=1,
taup=2,
ntc=2,
ntf=2,
iwrap=1,
barostat=1,
ntt=1, temp0=300.0, gamma_ln=0.0,
nstlim=2500, dt=0.002,
ntpr=100,ntxo=1,ntwr=100,ntwx=100,ntr=0,ig=19,
ibelly=1,
bellymask = ":WAT",
nmropt=1,
/
&wt type='TEMP0', istep1=0, istep2=2500,value1=300.0, value2=300.0
/
&wt type='END'
/
I really appreciate any suggestion.
Thanks in advance.
--
Danilo González Forero, MSc.
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Received on Fri Oct 27 2017 - 09:30:03 PDT
