<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 28/03/2011 7:06 PM, michael zhenin wrote:
<blockquote
cite="mid:AANLkTimg05rs3_sU+oF3hqvkZ66K-pGcqQkiN_3ZgBvj@mail.gmail.com"
type="cite">
<div dir="rtl">
<div style="text-align: left; font-family:
arial,helvetica,sans-serif;">
<div dir="ltr" style="text-align: left;"><font size="2">Dear
all,<br>
</font><font size="2">I am trying to run dynamics (mdrun) on
GROMACS 4.5.3 in parallel on 8 processors, but it crashes
after a while and refuses to reach to the end. <br>
</font><font size="2">
The error note that pops out is:<br>
<br>
</font></div>
<div dir="ltr" style="text-align: left;"><font size="2">1
particles communicated to PME node 4 are more than 2/3
times the cut-off<br>
<br>
</font><font size="2">>> out of the domain
decomposition cell of their charge group in dimension y.<br>
<br>
</font><font size="2">>> This usually means that your
system is not well equilibrated<br>
</font></div>
</div>
</div>
</blockquote>
<br>
So either your system is not well equilibrated, or your topologies
don't match reality. See
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a><br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTimg05rs3_sU+oF3hqvkZ66K-pGcqQkiN_3ZgBvj@mail.gmail.com"
type="cite">
<div dir="rtl">
<div style="text-align: left; font-family:
arial,helvetica,sans-serif;">
<div dir="ltr" style="text-align: left;"><font size="2">My
system contains protein, ATP and Mg. I have equilibirated
it for 300 ps that were divided into 3 parts. <br>
</font><font size="2">The first 2 parts were the NVT
equilibiration (the first one was made in order to </font><font
size="2">equilibrate only the water) - 100 ps each.<br>
<br>
</font><font size="2"><br>
</font><font size="2">The third was the NPT - 100 ps.<br>
</font><font size="2">The system wasn't constraint.<br>
<br>
</font><font size="2">My mdp file is :<br>
</font><font size="2"> <br>
</font><font size="2">title = OPLS wt nbd1 MD <br>
</font><font size="2">; Run parameters<br>
</font><font size="2">integrator = md ; leap-frog integrator<br>
</font><font size="2">nsteps = 20000000 ; 1 * 20000000 =
20000 ps, 20 ns<br>
<br>
</font><font size="2"><br>
</font><font size="2">dt = 0.001 ; 1 fs<br>
</font><font size="2">; Output control<br>
</font><font size="2">nstxout = 20000 ; save coordinates
every 2 ps<br>
</font><font size="2">nstvout = 20000 ; save velocities
every 2 ps<br>
</font><font size="2">nstxtcout = 20000 ; xtc compressed
trajectory output every 2 ps<br>
</font><font size="2">nstenergy = 20000 ; save energies
every 2 ps<br>
<br>
</font><font size="2"><br>
</font><font size="2">nstlog = 20000 ; update log file every
2 ps<br>
</font><font size="2">; Bond parameters<br>
</font><font size="2">continuation = yes ; Restarting after
NPT<br>
</font><font size="2">; Neighborsearching<br>
</font><font size="2">ns_type = grid ; search neighboring
grid cels<br>
</font><font size="2">nstlist = 5 ; 10 fs<br>
</font><font size="2">rlist = 1.0 ; short-range neighborlist
cutoff (in nm)<br>
<br>
</font><font size="2"><br>
</font><font size="2">rcoulomb = 1.0 ; short-range
electrostatic cutoff (in nm)<br>
</font><font size="2">rvdw = 1.0 ; short-range van der Waals
cutoff (in nm)<br>
</font><font size="2">; Electrostatics<br>
</font><font size="2">coulombtype = PME ; Particle Mesh
Ewald for long-range electrostatics<br>
</font><font size="2">ewald_rtol = 1e-05<br>
<br>
</font><font size="2"><br>
</font><font size="2">fourierspacing = 0.12 ; grid spacing
for FFT<br>
</font><font size="2">pme_order = 6 ;<br>
</font><font size="2">; Temperature coupling is on<br>
</font><font size="2">tcoupl = V-rescale ; modified
Berendsen thermostat<br>
</font><font size="2">tc-grps = Protein Non-Protein ; two
coupling groups - more accurate<br>
<br>
</font><font size="2"><br>
</font><font size="2">tau_t = 0.1 0.1 ; time constant, in ps<br>
</font><font size="2">ref_t = 300 300 ; reference
temperature, one for each group, in K<br>
</font><font size="2">; Pressure coupling is on<br>
</font><font size="2">pcoupl = Parrinello-Rahman ; Pressure
coupling on in NPT<br>
</font><font size="2">pcoupltype = isotropic ; uniform
scaling of box vectors<br>
<br>
</font><font size="2"><br>
</font><font size="2">tau_p = 1.0 ; time constant, in ps<br>
</font><font size="2">ref_p = 1.0 ; reference pressure, in
bar<br>
</font><font size="2">compressibility = 4.5e-5 ; isothermal
compressibility of water, bar^-1<br>
</font><font size="2">; Periodic boundary conditions<br>
</font><font size="2">pbc = xyz ; 3-D PBC<br>
<br>
</font><font size="2">; Dispersion correction<br>
<br>
</font><font size="2">DispCorr = EnerPres ; account for
cut-off vdW scheme<br>
</font><font size="2">; Velocity generation<br>
</font><font size="2">gen_vel = no ; Velocity generation is
off<br>
</font><font size="2">morse = yes<br>
<br>
<br>
</font><font size="2">I've searched the net for this error
and didn't find any answer. Did anybody see this error?
and what should i do with it..<br>
<br>
Thanks,<br>
<br>
Michael<br>
<br>
</font></div>
</div>
</div>
</blockquote>
<br>
</body>
</html>