Thanks for the reply. <br><br>Would that cause any problems in the simulation? It says force 154.9%, does that mean it is applying the wrong force? Is it safe to proceed to simulation like that?<br><br>Thanks,<br>Nihal<br>
<br><div class="gmail_quote">On Thu, Jun 16, 2011 at 9:54 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;">
<u></u>
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 17/06/2011 12:44 PM, E. Nihal Korkmaz wrote:
<blockquote type="cite">Hi all,<br>
<br>
I am trying to run GB model simulation of a small protein. I keep
getting these errors for every step printed to the log file.<br>
<br clear="all">
DD load balancing is limited by minimum cell size in dimension X<br>
DD step 35999 vol min/aver 0.799! load imb.: force 154.9%<br>
</blockquote>
<br></div>
Not all systems can efficiently parallelize on arbitrary numbers of
processors for a given implementation. There's an analysis at the
top of the .log file that describes the issues leading to the
minimum cell size. Possibly there's an issue there, but more likely
you've got not enough work for your processors.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">Below i copied my mdp parameters. I'd appreciate any
suggestion to help me fix this.<br>
<br>
Thanks,<br>
Nihal<br>
<br>
<br>
integrator = sd<br>
tinit = 0<br>
dt = 0.002<br>
nsteps = 5000000<br>
simulation_part = 1<br>
init_step = 1 %start from 5ns<br>
<br>
<br>
nstxout = 5000<br>
nstvout = 5000<br>
nstenergy = 500<br>
nstxtcout = 500<br>
nstlog = 500<br>
<br>
xtc_grps = System<br>
energygrps = System<br>
comm_mode = Linear<br>
; neighbor searching and vdw/pme setting up<br>
nstlist = 10<br>
ns_type = grid<br>
pbc = xyz<br>
rlist = 2.0<br>
<br>
coulombtype = pme<br>
fourierspacing = 0.1<br>
pme_order = 6<br>
rcoulomb = 2.0<br>
<br>
vdwtype = Cut-off<br>
rvdw_switch = 1.0<br>
rvdw = 2.0<br>
<br>
; cpt control<br>
tcoupl = Berendsen<br>
tc-grps = System<br>
tau_t = 0.1<br>
ref_t = 300.0<br>
Pcoupl = Berendsen<br>
pcoupltype = isotropic<br>
tau_p = 1.0<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
<br>
; velocity & temperature control<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
annealing = no<br>
constraints = hbonds<br>
constraint_algorithm = lincs<br>
morse = no<br>
<br>
<br>
-- <br>
Elif Nihal Korkmaz<br>
<br>
Research Assistant <br>
University of Wisconsin - Biophysics <br>
Member of Qiang Cui & Thomas Record Labs<br>
1101 University Ave, Rm. 8359<br>
Madison, WI 53706<br>
Phone: <a href="tel:608-265-3644" value="+16082653644" target="_blank">608-265-3644</a><br>
Email: <a href="mailto:korkmaz@wisc.edu" target="_blank">korkmaz@wisc.edu</a><br>
<br>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
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Research Assistant <br>University of Wisconsin - Biophysics <br>Member of Qiang Cui & Thomas Record Labs<br>1101 University Ave, Rm. 8359<br>
Madison, WI 53706<br>
Phone: 608-265-3644<br>
Email: <a href="mailto:korkmaz@wisc.edu" target="_blank">korkmaz@wisc.edu</a><br><br><br>