Yongchul Chung wrote:
I think your box is too small. try changing them.
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.
-Justin
On Tue, Oct 13, 2009 at 8:05 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Nilesh Dhumal wrote:
Hello,
I am trying to equilibrate glucose in water using Gromacs
4.0.5 version. I am geting the error immidiately after the
mdrun starts
Warning: 1-4 interaction between 1 and 18 at distance 3.462 which is
larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
p0_4238: p4_error: interrupt SIGSEGV: 11
Killed by signal 2.
Have you searched the website? You would have undoubtedly found this:
http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off
You should also search the list archive. This problem shows up
weekly, if not daily sometimes.
Is the problem in mdp file?
Nothing seems obviously wrong.
-Justin
Nilesh
Here is my pr.mdp file
title = cpeptid position restraining
cpp = /usr/bin/cpp
constraints = none
integrator = md
dt = 0.002 ; ps !
nsteps = 200000 ; total 1.0 ps.
nstcomm = 1
nstxout = 10
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
vdwtype = cut-off
rcoulomb = 1.0
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on
Tcoupl = Berendsen
tau_t = 0.1
tc-grps =system
ref_t = 350
; Pressure coupling is on
Pcoupl = Berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 350.0
gen_seed = 173529
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
