[gmx-users] Force displacement curve in SMD simulation

Justin Lemkul jalemkul at vt.edu
Fri Mar 23 20:12:38 CET 2018

On 3/23/18 3:07 PM, Parthiban Marimuthu wrote:
> Thank you for your 45 seconds.
> Before, posting the query, i read the materials in few other papers too and
> still found hard understand as a biologist, where to find the X
> displacement values from the whole bunch of files, when i perform SMD
> simulation for first time.

You won't necessarily have it automatically, depending upon what you 
want to look at. One can use the formula in that paper to compute the 
displacement of the spring, or the displacement may be expressed in 
terms of the separation of the two restrained species, which requires a 
separate calculation, performed by gmx distance. Then, one can assemble 
the plot that was shown in the paper.


> Parthiban Marimuthu.
>   Message: 1
>> Date: Fri, 23 Mar 2018 16:10:45 +0100
>> From: Joe Jordan <e.jjordan12 at gmail.com>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Force displacement curve in SMD simulation
>> Message-ID:
>>          <CAN-nNVOisCstOVBqP8mWnSWRF0hPE1FmWa3qGLRCTnc6AQsHaA at mail.gmail.
>> com>
>> Content-Type: text/plain; charset="UTF-8"
>> Try reading the methods section of the paper. I looked for ~45 seconds and
>> found it.
>> Joe Jordan


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

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