Nilesh Dhumal wrote:
I am using the opls parameters from Lope's paper.
In vaccum energy minimzatin is working well. MD is not at all working.
My other systems are running well. In the present system I changed the
anion, cation parameters are fine.
Is the problem with anion parameters?
If it's something you've changed, and all the other components are working, then
yes, I would suspect that there's likely a problem with whatever you've changed.
Please do consult the link I posted - it contains a "greatest hits" of sorts
of the most useful advice I can come up with for diagnosing unstable systems.
-Justin
Nilesh
On Fri, June 4, 2010 10:20 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I am trying to equilibrate my system, ionic liquids. My simulations
gets stop immediately. I reduced the step size. I modified initial
structure. I changed the box size. I checked force field parameters. I
am using opls foce field. I repeated my energy minimization 2-3 times. I
could not solve the problem. Every time i am geting following error
message.
step 0Warning: 1-4 interaction between 20 and 27 at distance 3.803
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 Segmentation fault
Can you tell me how to solve this problem.
Please consult the following:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an
_Unstable_System
The prime suspect in my mind is your topology. How have you validated
the parameters for your ionic liquids? Does in vacuo minimization and
short MD of each component separately run stably? While OPLS is quite
versatile, parameterizing ionic liquids properly is not a trivial task,
and is probably not very straightforward.
-Justin
Here I have pasted the eqilibration file.
Nilesh
title = cpeptid position restraining cpp
= /usr/bin/cpp
constraints = none integrator = md dt
= 0.001 ; ps !
nsteps = 100000 ; total 1.0 ps. nstcomm =
1
nstxout = 10000 nstvout = 10000 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 = v-rescale
tau_t = 0.1 tc-grps =system ref_t = 300 ; Pressure coupling is on
Pcoupl = parrinello-rahman
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 = 300.0 gen_seed
= 173529
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
