<br>
I strongly sugest you to try double precision compilation<br>
for energy conservation in NVE.<br>
<br>
Single precision is enough for NPT/NVT due to <br>
convenient algorithms (velocity and volume reescaling)<br>
that keeps the system at the desired termodynamic state<br>
(constante pressure and constante temperature) masking<br>
the truncation errors of the single precision simulation.<br>
<br>
In NVE no algorithm is used, so the double precision <br>
is necessary to prevent/postpone energy drift due to<br>
this error acumulation.<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;">
> Have you compiled gromacs in single precision?<br>> I think double precision compilation is critical<br>> for energy conservation in NVE.<br><br>Yes, I have used only single precision compilation because it has been enough
<br>accurate until now (NPT/NVT). Actually I just want to know if employed time<br>step of 2fs is applicable and so I think that I should use same compilation<br>also for energy conservation simulation in NVE ensemble. Or may I prove
<br>suitability of this long time step with double precision compilation even I<br>have done other simulations with single precision compilation?<br><br>Janne<br><br><br>> 2006/2/16, Janne Hirvi <<a href="mailto:janne.hirvi@joensuu.fi">
janne.hirvi@joensuu.fi</a>>:<br>> ><br>> > Hello!<br>> ><br>> > I have read several messages about energy conservation problems and<br>> > solutions<br>> > but however I am not sure if I have done something stupid. I have used
<br>> > time<br>> > step of 2.0fs for rigid SPC and SPC/E water models in simulations of bulk<br>> > water<br>> > (NPT) and water droplets on frozen polymer surfaces (NVT). Everything<br>> > 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
<br>> > (total<br>> > time 500ps) resulted in huge drift in total energy. I used same parameters<br>> > 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
<br>> > 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<br>> > long<br>> > but however other results from NPT bulk simulations are reasonable.<br>
> > 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<br>> > 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>> ><br>><br>------------------------------------------------------------------------------<br>> > Janne Hirvi, MSc(Physical Chemistry), Researcher<br>> > University of Joensuu, Department of Chemistry,
P.O.Box 111 80101 Joensuu,<br>> > 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>> ><br>> ><br>><br>------------------------------------------------------------------------------<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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