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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 27 2017 - 09:30:03 PDT
