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
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
--
========================================
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
