[gmx-users] Umbrella Sampling - no PMF plateau

[Steven Neumann]

Hi Brian,

Thanks for this. I checked many windows and I have not observed any
unphysical behaviour. I do not have any solvent, its a "water-free force
field" we have developed for the specific system. I do have freely moving
LJ beads though. I am thinking i may be the positions restraints dynamics
fault....but still not clue.

Steven


On Tue, Aug 5, 2014 at 11:04 PM, Brian Yoo <Brian.S.Yoo.12 at nd.edu> wrote:

> Hi Steven,
>
> I've run into a similar issue with CG simulations using tabulated
> potentials. For my system it turns out the continuous increase in PMF was
> due to the system "freezing" for some unknown reason. Once I annealed the
> system (~500 K) and messed around with the temperature coupling, the system
> unfroze, and I was eventually able to obtain the correct plateau in the PMF
> curve.
>
> Have you checked some of your configurations to see whether your system
> shows unphysical ordering? (I am assuming you are using an explicit
> solvent.)
>
> Hope this helps,
> Brian
>
>
> On Tue, Aug 5, 2014 at 5:19 AM, Steven Neumann <s.neumann08 at gmail.com>
> wrote:
>
> > Dear Gmx Users,
> >
> > I run US simulations between 2 nanotubes with attached proteins with
> > distance as a reaction coordinate. This is a coarse-grain simulation,
> both
> > tubes are placed across pbc so infinite in length. I have tabulated
> > potentials for both bonded and non-bonded interactions. I observed that
> > even at large distances between them in US windows when they do not
> > interact (even across pbc) the PMF is still increasing... no plateau is
> > observed...
> > I tried it in many systems increasing the box size but still the same
> > happening. The perido image is 15 nm away and the cutoff in potentials
> is 2
> > nm...
> >
> > Would you please advise? May that correspond to position restraint
> dynamics
> > of tube atoms of one of them (from which I pulled the other one)? Or
> maybe
> > tabulated potentials used?
> >
> > Steven
> > --
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