Hi Gustaf,
I’m not sure what equilibration protocol you’re using, but the one I use
generally does the trick, detailed here:
https://aip.scitation.org/doi/abs/10.1063/5.0013849
I also have a script that implements it for amber (it’s a bit rough around
the edges so use with care):
https://github.com/drroe/AmberMdPrep
Hopefully it is helpful.
-Dan
On Fri, Oct 23, 2020 at 5:26 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> I am experiencing some other problem, it seems that the OPC water
> simulation works as intended though a box with a capped hexapeptide and a
> Cl- ion does not.
>
> I have run 6 short simulations 3 with only water (OPC, SPCE and TIP3P) as
> well as 3 with the same water models as well as a hexapeptide and a
> chloride ion (FF14SP-SPCE, FF14SB-TIP3P and FF19SB-OPC).
>
> All systems with only water equilibrates nicely inside the timeframe. The
> pressure equilibration of OPC water is finished faster then the SPCE and
> TIP3P models and all simulation produce usable plots with the
> “process_m*.perl” scripts. Everything looks fine.
>
> The FF19SB-OPC system does NOT behave as intended. I can keep hammering
> this system with higher pressure and shorter taup though looking at the
> simulation, it seems like I am trying to equilibrate a block of ice with
> air trapped inside: https://gifyu.com/image/865p (Do note that I have NOT
> autoimaged with CPPTRAJ, the restricted motion of the water prevents
> changing the shape).
>
> Running only OPC water works just fine, so it seems that it is the FF19SB
> part which does not work as intended. For some reason, the entire system
> appears to be suffering from some motion restriction though I have
> implemented none. I have tried to see if the manual contained any
> information regarding particular options for input files or similar but did
> not find anything.
>
> I used the same input for all simulations:
>
> Energy minimization, 5000 steps SD then 5000 CG
> &cntrl
> imin=1,
> maxcyc=10000,
> ncyc=5000,
> ntb=1,
> cut=9.0,
> /
>
> 125 ps to constant T
> &cntrl
> ig =-1,
> imin = 0,
> iwrap = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 9.0,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 293.15,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 62500, dt = 0.002,
> ntpr = 1000, ntwx = 1000, ntwr = 2000
> /
>
> Constant T, pressure eq: 500 ps MD
> &cntrl
> ig =-1,
> imin = 0,
> iwrap = 0,
> irest = 1,
> ntx = 5,
> ntb = 2,
> pres0 = 1,
> ntp = 1,
> barostat = 1,
> taup = 2.0,
> cut = 9.0,
> ntc = 2,
> ntf = 2,
> tempi = 293.15,
> temp0 = 293.15,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 250000, dt = 0.002,
> ntpr = 1000, ntwx = 1000, ntwr = 2000
> /
>
> All the intended output files are produced and seemingly (except for the
> restricted motion) looks normal and reads just fine in cpptraj and vmd.
>
> Any ideas regarding what I am doing wrong?
>
> Best regards
> // Gustaf
>
>
> > On 22 Oct 2020, at 15:06, Carlos Simmerling <carlos.simmerling.gmail.com>
> wrote:
> >
> > Dave - no I haven't tried that during equilibration, since tighter
> coupling
> > fixes it I just made it part of our equilibration protocol long ago and
> > moved on. I'll try that since I have a sample setup with a bubble and see
> > if it works better.
> > carlos
> >
> > On Thu, Oct 22, 2020 at 8:48 AM David A Case <david.case.rutgers.edu>
> wrote:
> >
> >> On Wed, Oct 21, 2020, Carlos Simmerling wrote:
> >>
> >>> what is your pressure coupling constant? I often get vacuum bubbles
> unless
> >>> I include a step in my equilibration with tight coupling, taup around
> 0.1
> >>> or smaller.
> >>
> >> Carlos: have you ever tried barostat=2? It would be interesting to know
> >> if that makes a difference. Also, what is your starting density? If
> >> you use a closeness parameter of 0.7--0.8 (in solvateBox or solvateOct),
> >> you'll get a higher starting density, which might(?) reduce the tendency
> >> to get bubbles.
> >>
> >> ....dac
> >>
> >>
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Received on Fri Oct 23 2020 - 03:00:03 PDT
