<div dir="ltr">This is not a development question, so please direct it to gmx-users instead.<div><br></div><div>To understand differences between Gromacs versions, and in particular why it's likely a very bad idea to use Gromos force fields, read the release notes.</div><div><br></div><div>Cheers,</div><div><br></div><div>Erik</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Sep 5, 2019 at 11:46 AM Liu, Y. <<a href="mailto:y.liu@rug.nl">y.liu@rug.nl</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi there,<div> I have a question about tabulated force field: what is the difference when the tabulated potential and build-in potential are used in Gromacs simulations? why they give different results?<br><div> I simulate a DPPC membrane with Gromos force field. I use standard gromos input parameters in the simulation, but the area per lipid (0.630 (0.008) nm2) is different from when I compute it with tabulated force field(0.613 (0.007)nm2). This difference also exist when I use MARTINI force field.</div><div> I have use gmx dump -s *.tpr > comparison.xvg in two cases(build-in and tabulated potential) to make sure that the only difference in two scenarios is the tabulated potential. Here is the difference:</div><div>< coulombtype = Reaction-Field<br>---<br>> coulombtype = User<br>40,41c40,41<br>< epsilon-rf = 62<br>< vdw-type = Cut-off<br>---<br>> epsilon-rf = 1<br>> vdw-type = User<br>164c164<br>< tau-t: 0.1 0.1 0.1<br>---<br>> tau-t: 0.01 0.1 1<br>169c169<br>< energygrp-flags[ 0]: 0 1<br>---<br>> energygrp-flags[ 0]: 2 1<br></div><div> Then you may think my tabulated potential is problematic. However, I have used Gromacs 4.* with -debug flag to output the tabulated potential. Therefore, the tabulated potential should be correct. </div><div> In the output .edr file, I also found that the tabulated potential simulation cannot offer correct temperature for lipids as indicated in the thermal stat. At least, with the same parameters, it works well in the build-in potential simulation.</div><div> I do not understand where is the problem and what is the difference between the tabulated potential and build-in potential in Gromacs. Maybe it use different engine to compute the force?</div><div> Looking forward to your reply. Thank you.</div><div>regards</div><div>Liuyang</div><div> </div></div></div>
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