<div>Hi Michael:</div><div><br></div><div> Thanks for the reply! I did the following command: g_analyze -f energy.xvg -ac out.xvg</div><div><br></div><div>and in out.xvg I saw the following lines, it seems like a autocorrelation decrease over time. Does that mean the autocorrelation time here is infinite? Thanks</div>
<div><br></div><div>Steve</div><div><br></div><div><div># This file was created Fri Mar 11 16:46:01 2011</div><div># by the following command:</div><div># g_analyze -f energy.1.xvg -ac crap.xvg</div><div>#</div><div># g_analyze is part of G R O M A C S:</div>
<div>#</div><div># God Rules Over Mankind, Animals, Cosmos and Such</div><div>#</div><div>@ title "Autocorrelation"</div><div>@ xaxis label "Time (ps)"</div><div>@ yaxis label "C(t)"</div>
<div>@TYPE xy</div><div> 0.000 1.00000</div><div> 0.100 0.12191</div><div> 0.200 0.04696</div><div> 0.300 0.05139</div><div> 0.400 0.08079</div><div> 0.500 0.06953</div><div>
0.600 0.07639</div><div> 0.700 0.07060</div><div> 0.800 0.07970</div><div> 0.900 0.07947</div><div> 1.000 0.06976</div><div> 1.100 0.07309</div><div> 1.200 0.06973</div>
<div> 1.300 0.07161</div><div> 1.400 0.07008</div><div> 1.500 0.06880</div><div> 1.600 0.06747</div><div> 1.700 0.06574</div><div> 1.800 0.06383</div><div> 1.900 0.06175</div>
<div> 2.000 0.06125</div><div> 2.100 0.06316</div><div> 2.200 0.06383</div><div> 2.300 0.06076</div><div> 2.400 0.05812</div><div> 2.500 0.05635</div><div> 2.600 0.05565</div>
<div> 2.700 0.05727</div><div> 2.800 0.05663</div><div> 2.900 0.05746</div><div> 3.000 0.05641</div><div> 3.100 0.05375</div><div> 3.200 0.05202</div><div> 3.300 0.05316</div>
<div> 3.400 0.05255</div><div> 3.500 0.05047</div><div> 3.600 0.05019</div><div> 3.700 0.05199</div><div> 3.800 0.05144</div></div><div><br></div><div>......</div><div><br></div><div>
<br></div><br><br><div class="gmail_quote">On Fri, Mar 11, 2011 at 4:18 PM, Michael Shirts <span dir="ltr"><<a href="mailto:mrshirts@gmail.com">mrshirts@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im">> I am doing free energy calculation in Gromacs and want to get an error<br>
> estimate of my results. Is it possible to compute the autocorrelation time<br>
> of dVpot/dlambda in Gromacs using a certain length of trajectory such as 10<br>
> ns? Thanks a lot<br>
<br>
</div>The amount of simulation time required to compute the autocorrelation<br>
time of dVpot/dlambda will depend on the timescale of the system. You<br>
should be able to use g_analyze to analyze the energy.xvg output, and<br>
get an autocorrelation time. If your simulation time is 50x longer<br>
than the autocorrelation time, then you are very likely converged.<br>
However, if there are very long correlation times, you still might not<br>
have captured all of the time dependent variations in Vpot/dlambda.<br>
</blockquote></div><br>