[gmx-users] plot force vs time

[Justin Lemkul]

On 10/27/17 1:32 PM, abhisek Mondal wrote:
> 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.

That's what I plotted, and it's in the pullf.xvg file produced by mdrun.

-Justin

> 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
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================