[gmx-users] Umbrella_pull_simulation

[shahid nayeem]

Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal
-histo. But now  as suggested by you I added -b 1000 -e 10000 leaving 1ns
for equilibriation. The new profile.xvg is attached. How can I further
improve it.

Shahid Nayeem

On Tue, Feb 21, 2012 at 1:04 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> shahid nayeem wrote:
>
>> I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling
>> was done. The umbrella pullcode used is as follows.
>> ; Pull code
>> pull            = umbrella
>> pull_geometry   = distance  ; simple distance increase pull_dim        =
>> Y    N Y
>> pull_vec1       = 0.75 0 1
>> pull_start      = yes       ; define initial COM distance > 0
>> pull_ngroups    = 1
>> pull_group0     = Chain_B pull_group1     = Chain_A pull_rate1      =
>> 0.01      ; 0.01 nm per ps = 10 nm per ns
>> pull_k1         = 1000      ; kJ mol^-1 nm^-2
>>
>> Please tell me my profile.xvg and histo.xvg are fine or not. In
>> profile.xvg why i am not getting smooth convergence.
>>
>
> They're not terrible, but could be better.  The PMF profile is a little
> rough and there are some regions of the reaction coordinate with little
> sampling. Maybe your simulations need to be longer and/or you need to
> exclude some amount of time at the beginning of each as equilibration
> (which you probably should do anyway, but without seeing your g_wham
> command, there's no way to know what you may or may not be considering).
>
> -Justin
>
>  Shahid Nayeem
>>
>>
>> On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    shahid nayeem wrote:
>>
>>        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
>>
>>
>>    I will have to assume you mean nm.  Gromacs does not deal in
>>    Angstrom, and these distances would be within any sensible
>>    short-range cutoff and thus not indicative of actual separation.
>>
>>
>>        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.
>>
>>
>>    Sorry, I don't have a photographic memory, nor can I recall if
>>    you've ever posted your .mdp file, or at the very least, told us how
>>    much sampling you've done in each window.  It may well be that your
>>    simulations are simply too short to observe adequate
>>    post-equilibration sampling.
>>
>>
>>    -Justin
>>
>>    --     ==============================**__==========
>>
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
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> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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