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. <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">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 class="im">
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 class="im">
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 class="im"><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>-- <br>Ilya Chorny Ph.D.<br><br>
</div></div>