[gmx-users] Umbrella_pull_simulation

shahid nayeem msnayeem at gmail.com
Mon Feb 20 05:17:11 CET 2012

Thanks Justin
I have pulled one of the chain from an initial COM distance value of 3.65 A
to 7.90 A. When I look this trajectory in VMD I find that the chain is
completely separated. But even at this separation the profile.xvg file does
not show its convergence to one value. I sent this file to you earlier.
shahid Nayeem

On Sat, Feb 18, 2012 at 7:27 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> shahid nayeem wrote:
>> Dear All
>> I am doing umbrella sampling for a protein complex. After analysis I am
>> finding that prifle.xvg has not converged. Now I want to extend simulation.
>> I have already pulled one chain to the length of the box. Can I further
>> pull by extending the box size and add more windows to umbrella sampling.
>> Please suggest.
> You would have to use a simple test system to prove that this is a valid
> approach.  Changing the nature of the system for some windows sounds very
> questionable to me, and likely would be to reviewers.
>  How one should ascertain the initial box size so that g_wham gives a
>> converged profile.xvg.
> You should determine the distance needed to sufficiently separate your
> components, that is, determine the minimum COM distance at which
> interaction between the two species is negligible.  Ideally, they would be
> non-interacting, but with PME, that is not possible.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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