I jumped to the conclusion too fast. Thanks Justin for correcting me. Disregard my previous comment please.<br><br><div class="gmail_quote">On Tue, Oct 13, 2009 at 10:35 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>
Yongchul Chung 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 think your box is too small. try changing them.<br>
<br>
</blockquote>
<br></div>
What leads you to this conclusion? We have no information about the box. Presumably, the only box that is "too small" would be one that doesn't satisfy the minimum image convention, but grompp fails with a fatal error in that case.<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;"><div><div></div><div class="h5">
On Tue, Oct 13, 2009 at 8:05 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Nilesh Dhumal wrote:<br>
<br>
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<br>
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>
<br>
Have you searched the website? You would have undoubtedly found this:<br>
<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>
You should also search the list archive. This problem shows up<br>
weekly, if not daily sometimes.<br>
<br>
<br>
Is the problem in mdp file?<br>
<br>
<br>
Nothing seems obviously wrong.<br>
<br>
-Justin<br>
<br>
<br>
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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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
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<br>
-- <br>
Yongchul "Greg" Chung<br>
Graduate Student<br>
Dept. of Chemical Engineering, Case Western Reserve University<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <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>
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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>