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

[shivangi nangia]

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.

Thanks,
sxn

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


On Fri, Jan 24, 2014 at 3:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/24/14, 2:34 PM, shivangi nangia wrote:
>
>> Hello,
>>
>> I wish to perform umbrella sampling without using the pull code.
>> I have varied starting configurations for protein-bilayer.
>>
>> Is there any advantage(s) of doing a manual pull versus the pull code or
>> vice-versa?
>> What is the reason to do it with pull force?
>>
>>
> I think you need to provide more detail on what you are doing or are
> planning to do.  What is manual pulling?
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
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