I managed to run my simulation but which kind of coulomtype can I use except PME? also I get different averages for kinetic and potential energies than before reducing units I think these numbers must be the same because E*=E/epsilon (epsilon is about 0.9977) for argon. could u please help me about this issue?( I have reduced box size, dt, C6=4 , C12=4, mass=1 and temperature. before reducing temperature is 300 and after reducing it is 2.5)<br>
<br><div class="gmail_quote">On Sun, Jan 16, 2011 at 12:23 AM, 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">On 15/01/2011 8:50 PM, leila separdar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard Jones potential in a cubic box with linear size of 3.34. but when I reduced units I confront with this error<br>
Back Off! I just backed up md.log to ./#md.log.5#<br>
Reading file argon.tpr, VERSION 4.0.7 (single precision)<br>
<br>
Back Off! I just backed up argon.trr to ./#argon.trr.3#<br>
<br>
Back Off! I just backed up ener.edr to ./#ener.edr.3#<br>
starting mdrun 'Built with Packmol'<br>
1000000 steps, 1000.0 ps.<br>
Segmentation fault<br>
</blockquote>
<br></div>
What was your command line? What does the end of the logfile say? Why are you using PME for an LJ simulation that presumably has no electrostatic interactions?<br>
<br>
Mark<div><div></div><div class="h5"><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>
there is no error in energy minimization or grommp command. could u please help me?<br>
here is my md.out file iin reduced units.<br>
cpp = /usr/bin/cpp<br>
integrator = md<br>
dt = 0.001<br>
nsteps = 1000000<br>
nstcomm = 100<br>
nstxout = 100<br>
nstvout = 100<br>
nstfout = 0<br>
nstlog = 100<br>
nstenergy = 100<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 2.9<br>
coulombtype = PME<br>
rcoulomb = 2.9<br>
rvdw = 2.9<br>
fourierspacing = 0.35<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
<br>
;Berendsen temperature coupling is on in three groups<br>
Tcoupl = berendsen<br>
tau_t = 0.1<br>
tc_grps = GAS<br>
ref_t = 2.5<br>
<br>
;generate velocities<br>
gen_vel = yes<br>
gen_temp = 2.5<br>
gen_seed = 173529 <br>
</blockquote>
<br></div></div><font color="#888888">
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