[gmx-users] Pull code vs. manual pull for umbrella sampling

[shivangi nangia]

Hello,

As I had explained earlier, I have done MD at varied protein bi-layer
distances.

I now want to create a probability distribution histogram along the
reaction coordinate I generated by varying the distances.

I know I can concatenate various .trr files I have from various MD runs
with different initial starting configurations.

Is there a way to obtain the probability distribution histogram.

Kindly help.

Thanks,
sxn



Shivangi Nangia, Ph. D
Postdoctoral Research Associate
Department of Molecular and Cell Biology
University of Connecticut


On Fri, Jan 24, 2014 at 3:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/24/14, 3:50 PM, shivangi nangia wrote:
>
>> Dear Justin,
>>
>> Okay, so I have multiple configurations of protein and bi-layer system (30
>> initial configurations) at varied distances (in steps of 0.05 nm).
>>
>> The protein has been moved away with respect to its COM.
>> So I have "manually" pulled the protein away from the bi-layer instead of
>> using
>> the pull code.
>>
>> I have run MD simulations for each of these configurations.
>>
>> I need to use g_wham to calculate the PMF and for that I need the
>> pullx.xvg files.
>>
>>
> It won't be possible.  What you did wasn't umbrella sampling, it was just
> MD. If there is no restraint potential applied during the simulations in
> each of the sampling windows, there's nothing to de-bias to reconstruct a
> free energy profile.
>
> You can generate the configurations in any manner you like (manually or by
> using the pull code), but the umbrella sampling itself requires the use of
> the pull code.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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