Dear List,
I have been running protein simulations using explicit water in AMBER16 and
have been using the stepwise minimization (water first followed by solute)
and then heating (NVT) followed by density equilibration (NPT). I am using
a similar protocol where protein is embedded 10 A above the GOLD surface.
Water is added on both sides of surface using tleap.
We tried running a short 200 ps NVT run with Gold and protein atoms fixed
(force constant of 2 kcal/mol A^2) however, upon visualization in VMD, we
notice holes/bubbles (on the edges of the box). One would expect very
little change in box dimension during NVT (holding atoms fixed). Is it an
artifact of applying restraints or something is wrong with solvation
protocol? We want to perform simulation where GOLD surface is always fixed.
Below is the protocol for minimization and NVT. I will appreciate your
reply.
//Minimize water and ions
&cntrl
imin = 1,ntmin=2,
maxcyc = 5000,
ncyc = 1000,igb=0,
ntpr=100,ntwx=100,
cut = 10,ntb=1,
ntr=1, restraintmask="!:WAT,Cl-",
restraint_wt=2,
/
System minimization: //minimize protein, water and ions
&cntrl
imin=1, ntmin=1, nmropt=0, drms=0.1
maxcyc=2000, ncyc=1500,
ntx=1, irest=0,
ntpr=100, ntwr=100, iwrap=0,
ntf=1, ntb=1, cut=10.0, nsnb=20,
igb=0,iwrap=1,
ntr=1, restraintmask=":Au",
restraint_wt=2,
&end
Heating System // Protein and Au atoms are fixed
&cntrl
imin=0, nmropt=1,
ntx=1, irest=0,
ntpr=500, ntwr=500, ntwx=500, iwrap=1,
ntf=2, ntb=1, cut=10.0,
igb=0,
ibelly=0, ntr=1,ig=-1,
nstlim=100000, nscm=500, dt=0.002,
ntt=3,gamma_ln=2,
tempi=100, temp0=310,
ntc=2,restraintmask='!:WAT,Cl-',
restraint_wt=2.0,
&end
&wt type='TEMP0', istep1=0, istep2=100000, value1=1, value2=310, &end
&wt type='END' &end
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 01 2017 - 00:00:03 PST
