Ok, I got it. Set electrostatics to PME-switch. Made rcoulomb-switch .1 less than rcoulomb and set rlist accordingly and now I am conserving energy. Yipee!!!<div><br></div><div>It did not make sense to me that the system had to be fully relaxed to conserve energy. It should conserve energy energy as long as it has been minimized and has no major clashes. <br>
<div><br></div><div>Thanks,</div><div><br></div><div>Ilya</div><div><br><br><div class="gmail_quote">On Wed, Mar 11, 2009 at 7:38 PM, Ilya Chorny <span dir="ltr"><<a href="mailto:ichorny@gmail.com">ichorny@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">If I plot the K.E(t) and P.E.(t) they are both going down. In an NVE simulation they should counter balance. I am leaking K.E. somewhere. I reran with a relaxed P.E(t) and saw the same behavior. This is happening both at 2 and 4 fs so its not a time step issue. Any thoughts? I thought it might be COM removal so I turned it off to no avail. <div>
<br><div>Any chance one of the Gromacs people can give me the mdp file from the DHFR simulation in the 4.0 paper. <div><div></div><div class="h5"><br><br><div class="gmail_quote">On Tue, Mar 10, 2009 at 10:21 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Ilya Chorny wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
Forgot column labels on energies. <br>
Average RMSD Fluct. Drift Tot-Drift<br>
2 fs time step Total Energy 46497.2 36445.6 2630.7 -148.833 -148833<br>
4 fs time step Total Energy 41580.8 37693.4 2856.08 -130.198 -130198<br>
<br></div><div>
On Tue, Mar 10, 2009 at 7:17 PM, Ilya Chorny <<a href="mailto:ichorny@gmail.com" target="_blank">ichorny@gmail.com</a> <mailto:<a href="mailto:ichorny@gmail.com" target="_blank">ichorny@gmail.com</a>>> wrote:<br>
<br>
Hello All,<br>
<br>
I am trying to run some calibration calculations with 2/4 fs time<br>
steps. I am trying to reproduce the results in the Gromacs 4.0 paper<br>
on a protein/water (not the same protein) system with ~100K atoms. I<br>
ran 1 ns simulation in the NVE ensemble. My mdp params are shown<br>
below. Topolgy was created using -vsite h. My system has 218441<br>
degrees of freedom according to GMXDUMP. My P.E. energy is ~ -1E5<br>
and has not full relaxed after 1ns but is close. <br>
2 fs time step Total Energy 46497.2 36445.6 2630.7 -148.833 -148833<br>
4 fs time step Total Energy 41580.8 37693.4 2856.08 -130.198 -130198<br>
<br>
Drift (kt/ns) 2fs/4fs = .34/.29<br>
<br>
The drift seems to be much larger for both the 2fs and 4fs time<br>
steps then in the paper. Do I have a clear bug in my params? Should<br>
I wait till the system fully relaxes before doing the drift calculation?<br>
</div></blockquote>
<br>
You should definitely equilibrate the system before trying to measure energy drift. I suggest doing so in NPT to fix your density and temperature, then switching to NVE, wait a bit, and only then start to collect your data.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
coulombtype = PME<br>
rcoulomb = 1.0<div><br>
fourierspacing = 0.12<br>
; FFT grid size, when a value is 0 fourierspacing will be used<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
; EWALD/PME/PPPM parameters<br>
pme_order = 4<br>
ewald_rtol = 1.e-04<br>
</div></blockquote>
<br>
I would think the ewald_rtol value used in the paper was 1e-5, but it is unfortunately not stated. The different numbers will lead to different costs and accuracies for the direct and FFT parts of the PME algorithm.<br>
<br>
rcoulomb, fourier_whatever, pme_order and ewald_rtol are all relevant if you're trying to reproduce results.<br>
<br>
Mark<br>
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</blockquote></div><br><br clear="all"><br></div></div>-- <br>Ilya Chorny Ph.D.<br><br>
</div></div>
</blockquote></div><br><br clear="all"><br>-- <br>Ilya Chorny Ph.D.<br><br>
</div></div>