Hi Sanku,<div>I was using the pullf.xvg and multiplying it with pulling rate and time.</div><div>f*v*dt = W</div><div>and getting the total work for each SMD simulation.</div><div><br></div><div>I'm not sure if this is the best/correct way to do it. But from original Jarzynski's article (PRL (2007) 78(14), 2690-2693) this is what I deduced. I asked this question but I think very few users of Gromacs do Jarzynski Equality (JE) to get free energy differences. </div>
<div><br></div><div>If anyone can comment on this, it will be useful for the community.</div><div><br></div><div>PS: If you use AMBER, it gives the work profile as the output. You can use the total work which is printed at the last line of the output and get the exponential average of beta*W.</div>
<div><br></div><div>PPS: May be you are aware of this issue, but the JE suffers from the fact that you do the exponential average and the smaller work values determine everything. </div><div><br></div><div><br></div><div>
Regards<br>Sai</div><div><br></div><div><br><br><div class="gmail_quote">On Fri, Nov 4, 2011 at 7:46 PM, Sanku M <span dir="ltr"><<a href="mailto:msanku65@yahoo.com">msanku65@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hi,</div><div>I am performing steered MD simulation using gromacs.</div><div> I was wondering how one can get the time profile of the irreversible work from the gromacs pull-code out put . From constant pulling-rate SMD, we get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying the the value from pullx.xvg and value from pullf.xvg will provide the work . Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate multiplied by time ?<br>
</div><font color="#888888"><div>Sanku</div></font></div></div><br>--<br>
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