Hi,
Are you sure you're not just seeing artifacts from PBC? If you have
solute sticking out of one side of the box, it can appear as if there
is a bubble in solvent on the other side when in reality the image of
the solute is there. You can check this in VMD by using the 'Periodic'
tab under 'Graphical Representations'.
-Dan
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
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Mar 01 2017 - 08:30:04 PST
