<br>
Have you compiled gromacs in single precision?<br>
I think double precision compilation is critical<br>
for energy conservation in NVE.<br>
<br><br><div><span class="gmail_quote">2006/2/16, Janne Hirvi <<a href="mailto:janne.hirvi@joensuu.fi">janne.hirvi@joensuu.fi</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello!<br><br>I have read several messages about energy conservation problems and solutions<br>but however I am not sure if I have done something stupid. I have used time<br>step of 2.0fs for rigid SPC and SPC/E water models in simulations of bulk water
<br>(NPT) and water droplets on frozen polymer surfaces (NVT). Everything seemed to<br>be just fine but when I tested energy conservation of bulk model in NVE<br>ensemble I was terrified.<br><br>NVE bulk simulation of 1372 rigid SPC water molecules with 2fs time step (total
<br>time 500ps) resulted in huge drift in total energy. I used same parameters as<br>for other simulations and even those aren't optimal I expected atleast<br>something better. Energy conservation seemed to be adequate only when I used as
<br>short time step as 0.5fs.<br><br><br>Time step (fs) Total Energy (kJ/mol) Drift<br><br>2.0
-45596.6
1235.5<br>1.0
-46147.5
330.974<br>0.5
-46331.1
<10 (not yet finished)<br><br><br>Parameters:<br><br>comm-mode = None or Linear<br>nstlist = 5 or 10<br>rlist =
1.2<br>coulombtype = PME<br>rcoulomb = 1.2<br>vdw-type = Cut-off<br>rvdw
= 1.2<br>fourierspacing = 0.12<br>pme_order = 4<br>ewald_rtol = 1e-05<br>ewald_geometry = 3d<br>tcoupl = No<br>Pcoupl = No<br><br><br>Bad energy conservation indicates that employed time step of
2.0fs is too long<br>but however other results from NPT bulk simulations are reasonable. Moreover I<br>think that its quite normal to use this long time step for rigid water<br>molecules. So I am willing to know if this large energy conservation problems
<br>are acceptable and are they atleast "partially compensated" in NPT or NVT<br>ensemble when temperature coupling prevents heating of the system?<br><br><br><br>Thanks for any help or comments!<br><br>Janne<br>
<br>------------------------------------------------------------------------------<br>Janne Hirvi, MSc(Physical Chemistry), Researcher<br>University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI<br>Tel: +358 13 2514544 & +358 50 3474223
<br>E-mail: <a href="mailto:Janne.Hirvi@joensuu.fi">Janne.Hirvi@joensuu.fi</a> & <a href="mailto:hirvi@cc.joensuu.fi">hirvi@cc.joensuu.fi</a><br>------------------------------------------------------------------------------
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