If you’d like, send me off-list your topology and the problematic
coordinates and I can check it out and try to reproduce the bad behavior,
and hopefully smoke out any bugs.
-Dan
On Fri, Oct 23, 2020 at 7:13 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> Thank you very much for the tips, I will look at them carefully as soon as
> I have time. I am sure I will have use for these at some point.
>
> Just to avoid confusion. This is a very small system with an initially
> linear, capped hexapeptide. I am doing energy minimisation, temperature
> equilibration and pressure equilibration with no restraints. I am aware of
> the basic idea for proteins/membranes, alternating restraining the movement
> of some structures while letting others move and so forth. My reservation
> is that this only system seems to have everything constrained though no
> restraints have been used whatsoever. The other systems using ff14SB with
> SPCE/TIP3P and the plain OPC water system are equilibrated using identical
> input so unless there is some input option not compatible with ff19SB, then
> the protocol should not be the cause of the observed behaviour.
>
> If the system did not equilibrate properly, that would be “fine”. Though I
> am getting nothing in the “process_m*.perl” scripts output regarding energy
> minimisation or pressure equilibration. Visually, there is no
> “diffusion”/spreading of waters. Everything seems to be “locked” in place,
> no water is displaying any expected degree of rotation or movement. The
> system is basically incompressible.
>
> I could try ff14SB-OPC and ff19SB-tip3p/spce to see if anything changes
> though was hoping that someone would notice some obvious mistake.
>
> Thank you again for suggestions and tips, it is greatly appreciated.
>
> I’ll keep trying
> Best regards
> // Gustaf
>
>
> > On 23 Oct 2020, at 11:36, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > 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
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> 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
> >>
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Received on Fri Oct 23 2020 - 04:30:02 PDT
