Hi,<br><br>
<div class="gmail_quote">
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">1- g_energy is giving #Surf*SurfTen by default. On the other hand surface tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e Pres-XX-(bar), Pres-YY(bar), Pres--(bar)<br>
<br>Can anyone tell me what the difference between these two is?<br></blockquote>
<div>They should be equal, bearing in mind units conversion. </div>
<div> </div>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br>2- In pressure coupling settings there is surface_tension option which I guess is applicable where surface tension needs to be kept fixed. If one want to calculate surface tension I dont think this option make sense. Am I right?<br>
</blockquote>
<div>Yes.</div>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br>3- I am using the following setting: I calculate the average for a 2ns run and different start times as shown below. Although T, P and other quantities are equilibrated after 200ps, surface tension is not giving a constant value. Is that because I am not using berenden P coupling? (As mentioned in the manual surface tension works with berendsen)<br>
<br>Pcoupl = Parrinello-Rahman <br>Pcoupltype = isotropic <br>tau_p = 1 1 <br>compressibility = 4.5e-5 <br>ref_p = 40 <br>
<br><br>time period for which average is calculated Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>1-2000 ps run: #Surf*SurfTen 6.43844 3588.74 3588.35 0.091406 182.721<br>
500-2000 ps #Surf*SurfTen 12.8518 3605.72 3605.26 0.132126 198.189<br>1000-2000ps #Surf*SurfTen 18.8821 3610.97 3610.8 0.11819 118.191<br>1500-2000ps #Surf*SurfTen 23.0072 3585.51 3584.93 -0.444037 -222.019<br>
<br></blockquote>
<div>This question is anything but trivial! Look at the RMSD values compared with the averages. The dispersion is so high that you can't be sure if this is or not equilibrated.</div>
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<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br>4- Assuming I am getting surface tension for a cubic box, to compare this with reported values in literature I need to divide by 6 (no. of surfaces)? <br>
</blockquote>
<div>No. You have to divide by the number of interfaces (2 for a bilayer immersed in water, for instance) </div>
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<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br>5- Does box six affect the results? (mine is 3.3 nm ).<br><br></blockquote>
<div>Yes, but see answer 3, above.</div>
<div> </div>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br>Thank you,<br><br><br><br><br><br><br><br><br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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