Hi David,<br>Is the paper[(David van der Spoel and Paul J. van Maaren: /The origin of layer<br>structure artifacts in simulation of liquid water/ J. Chem. Theor. Comp.<br>*2* pp. 1-11 (*2006*)) ]already published and available online?
<br><br>I tried to find it, but I could not get it.<br>If possible, can you forward that to the Discussion List?<br>Thanks a lot,<br>-Viswanadham<br><br><div><span class="gmail_quote">On 2/20/06, <b class="gmail_sendername">
David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Naser, Md Abu wrote:<br>><br>> Hi Viswanadham Sridhara and Michael Patra,<br>><br>> Thank you very much for your reply. I have solved the problem. It was<br>> just spc water model which dose not give good estimate of density at
<br>> room temperature. I am now using spce which is giving correct density<br>> even in vacuum.<br>><br>> Thanking you all,<br>><br>It's not as easy as that. Much depends on simulation conditions, for<br>instance the DispCorr = EnerPres also yields a density increase of 12-15
<br>g/l. A larger cut-off gives higher density, reaction field lower<br>density. Please do also check:<br><br>David van der Spoel and Paul J. van Maaren: /The origin of layer<br>structure artifacts in simulation of liquid water/ J. Chem. Theor. Comp.
<br>*2* pp. 1-11 (*2006*)<br><br>Not just to plug my own work, but because this stuff is not<br>straight-forward and you may get counter-intuitive results if you play<br>with the parameters without carefully checking the result. It is alway
<br>good practice to try to reproduce results from the literature!<br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br><br>_______________________________________________
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Graduate Research Assistant,<br>Old Dominion University, "VIRGINIA".<br>