<br><br><div class="gmail_quote">On 22 March 2011 22:46, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Elisabeth wrote:<div class="im"><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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On 22 March 2011 22:31, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
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Elisabeth wrote:<br>
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Hello,<br>
I did two simulations on the same system using versions 4.0.7<br>
and 4.5.3. It seems like the unit of surface tension is not the<br>
same in these versions because I am getting ~250 KJ/mol an in<br>
4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted<br>
into bar nm? Can anyone help please.<br>
<br>
<br>
Is this from g_energy output? In past versions, everything was<br>
printed as "kJ/mol," even quantities that obviously weren't, like<br>
temperature, pressure, etc.<br>
<br>
<br>
Yes, so why are the results so different. I am using exactly the same mdp file.! <br>
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</blockquote>
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Any pressure-related quantity is going to be subject to enormous fluctuations. This has been discussed within the last few days. Without seeing the .mdp file and a description of the system, it's hard for anyone to comment on what the results might mean.<br>
</blockquote><div><br>Thanks. I am working on a pure alkane system, in a box of 3X3X3 which is extended in Z to create liq/air interface. That is 3X3X6 . What could be reason for such a big difference in results from two version? Thanks alot! <br>
<br>integrator = md <br>dt = 0.002 <br>nsteps = 1000000 <br> <br>nstenergy = 100 <br>
nstxout = 100 <br>nstlist = 10 <br>ns_type = grid <br>coulombtype = PME <br>vdw-type = Shift <br>
rcoulomb-switch = 0 <br>rvdw-switch = 0 <br>rlist = 1.1 <br>rcoulomb = 1.1 <br>rvdw = 1.0 <br>
<br>fourierspacing = 0.12 <br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4 <br>ewald_rtol = 1e-5<br>;optimize_fft = yes<br>
<br>Tcoupl = v-rescale <br>tc-grps = System <br>tau_t = 0.1 <br>ref_t = 300 <br> <br>pbc = xyz <br>
<br>gen_vel = yes <br>gen_temp = 300.0 <br>gen_seed = 173529 <br><br>constraints = all-bonds <br>constraint-algorithm = lincs<br>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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