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.
-Justin
Parthiban Marimuthu. Message: 1Date: Fri, 23 Mar 2018 16:10:45 +0100 From: Joe Jordan <e.jjorda...@gmail.com> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force displacement curve in SMD simulation Message-ID: <CAN-nNVOisCstOVBqP8mWnSWRF0hPE1FmWa3qGLRCTnc6AQsHaA@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
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