[gmx-users] Umbrella Sampling - no PMF plateau

[Brian Yoo]

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>