You are getting classic vacuum bubbles. The water can move, so it
settles. This is to be expected, really. You should run NPT with
restraints on the solutes in order to collapse the bubbles. If the protein
and gold particle are at the center of your simulation cell, you probably
see pieces of a single bubble on various vertices or edges of your box.
That's surface tension at work :-)
If the box dimensions are critical, you can try estimating the volume of
the vacuum bubble, then use the AddToBox program to add a specific number
of waters to the dry system equal to the amount added by tleap plus the
rest you need (be sure to respect the protein and solute with a decent
value of -RP, so as not to let new waters be inserted too close to the
system of interest).
Happy solvating,
Dave
On Wed, Mar 1, 2017 at 2:35 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 01 2017 - 03:00:02 PST
