[gmx-users] plot force vs time

[abhisek Mondal]

Hello Justin,

Well, I'm trying to get the force-vs-time plot for different pulling rates
just to compare if the pattern of the plot remains the same. A similar kind
of plot I found in your article of JPCB, regarding the amyloid fibril
dissociation. I'm not totally sure but I think I'm looking for the force on
the spring.

Thank you.



On Fri, Oct 27, 2017 at 8:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/27/17 5:27 AM, abhisek Mondal wrote:
>
>> Hi,
>>
>>      I'm performing an umbrella sampling simulation with a protein ligand
>> system. For starter, I'm trying to pull the ligand with different rates.
>>
>>     How can I obtain the Force-vs-Time plot for each individual rate of
>> pulling performed ?
>>
>
> Force on what?  The spring?  That's in the pullf.xvg file.  If you want
> forces on atoms, you have to save them in the .trr and extract with gmx
> traj -of.
>
> -Justin
>
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-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*