I set nstlog = 100000000000, and still I get a 5MB log file within a minute of starting the sim. It seems absurd, but its happening :(<br><br><div class="gmail_quote">On Thu, Dec 16, 2010 at 10:05 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
Nimesh Jain wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
I am trying to simulate a system of 880 particles with implicit solvent using brownian dynamics, but the simulation generates huge log files (it writes md.log files at a rate of almost 5MB/minute) and this crashed my system since I ran out of space :(<br>
<br>
My mdp file looks like this:<br>
<br>
include =<br>
define =<br>
integrator = bd<br>
tinit = 0<br>
dt = 0.001<br>
nsteps = 100000000 ;100000<br>
simulation_part = 1<br>
init_step = 0<br>
comm-mode = Angular<br>
nstcomm = 1<br>
comm-grps =<br>
<br>
emtol = 0.01<br>
emstep = 1.5<br>
<br>
nstxout = 10000<br>
nstvout = 10000<br>
nstfout = 10000<br>
<br>
nstenergy = 1000<br>
<br>
nstxtcout = 1000<br>
xtc-precision = 1000<br>
<br>
nstlog = 0<br>
<br>
xtc-grps =<br>
energygrps =<br>
<br>
ns_type = grid<br>
pbc = xyz<br>
periodic_molecules = no<br>
<br>
rlist = 8.95<br>
<br>
coulombtype = user<br>
rcoulomb-switch = 0<br>
rcoulomb = 8.95<br>
epsilon-r = 1<br>
<br>
vdw-type = user ;cutoff<br>
rvdw-switch = 0<br>
rvdw = 8.95<br>
DispCorr = No<br>
table-extension = 1<br>
<br>
; Seperate tables between energy group pairs<br>
energygrps = A T G C P300 SA SB<br>
<br>
<br>
energygrp_table = A A A T A G A C A P300 A SA A SB T T T G T C T P300 T SA T SB G G G C G P300 G SA G SB C C C P300 C SA C SB P300 P300 P<br>
300 SA P300 SB SA SA SA SB SB SB<br>
<br>
; Spacing for the PME/PPPM FFT grid<br>
fourierspacing = 0.10<br>
<br>
Tcoupl = Nose-Hoover<br>
tc-grps = System<br>
tau_t = 0.001<br>
</blockquote>
<br></div></div>
This doesn't seem like a reasonable setting for tau_t; grompp should have warned you about that since dt = tau_t!<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
ref_t = 300.00<br>
<br>
Pcoupl = No<br>
<br>
andersen_seed = 815131<br>
<br>
gen_vel = yes<br>
gen_temp = 300.0000<br>
gen_seed = 1993<br>
<br>
Please let me know if there is a solution to write smaller mdp files. I have set nstlog = 0 , but even that doesn't work!<br>
</blockquote>
<br></div>
Set nstlog to some incredibly large number, then, and it will only output a few times. It seems strange that nstlog = 0 didn't suppress the .log file output as it would any of the other nst* settings.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Thanks<br>
Nimesh<br>
<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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