I think your box is too small. try changing them.<br><br><div class="gmail_quote">On Tue, Oct 13, 2009 at 8:05 PM, 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 class="im"><br>
<br>
Nilesh Dhumal wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
I am trying to equilibrate glucose in water using Gromacs<br>
4.0.5 version. I am geting the error immidiately after the mdrun starts<br>
Warning: 1-4 interaction between 1 and 18 at distance 3.462 which is<br>
larger than the 1-4 table size 2.400 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp file<br>
or with user tables increase the table size<br>
p0_4238: p4_error: interrupt SIGSEGV: 11<br>
Killed by signal 2.<br>
<br>
</blockquote>
<br></div>
Have you searched the website? You would have undoubtedly found this:<div class="im"><br>
<br>
<a href="http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off" target="_blank">http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off</a><br>
<br></div>
You should also search the list archive. This problem shows up weekly, if not daily sometimes.<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;">
Is the problem in mdp file?<br>
</blockquote>
<br></div>
Nothing seems obviously wrong.<br>
<br>
-Justin<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;">
Nilesh<br>
<br>
Here is my pr.mdp file<br>
title = cpeptid position restraining<br>
cpp = /usr/bin/cpp<br>
constraints = none<br>
integrator = md<br>
dt = 0.002 ; ps !<br>
nsteps = 200000 ; total 1.0 ps.<br>
nstcomm = 1<br>
nstxout = 10<br>
nstvout = 1000<br>
nstfout = 0<br>
nstlog = 10<br>
nstenergy = 10<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 1.0<br>
coulombtype = PME<br>
vdwtype = cut-off<br>
rcoulomb = 1.0<br>
rvdw = 1.4<br>
fourierspacing = 0.12<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>
; Berendsen temperature coupling is on<br>
Tcoupl = Berendsen<br>
tau_t = 0.1<br>
tc-grps =system<br>
ref_t = 350<br>
; Pressure coupling is on<br>
Pcoupl = Berendsen<br>
pcoupltype = isotropic<br>
tau_p = 0.5<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>
gen_temp = 350.0<br>
gen_seed = 173529<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
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</blockquote>
<br></div></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<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>
========================================<div><div></div><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Yongchul "Greg" Chung<br>Graduate Student<br>Dept. of Chemical Engineering, Case Western Reserve University<br>