Andrea Muntean wrote:
I am simulating one chain of PS. The box is produced by pdb2gmx. If I
run simulations with timestep 0.1 fs up to 0.4 fs everything seem to
be ok. With 1 fs (which should be a normal time for my system) I would
get the following warning:
Warning: 1-4 interaction between 290 and 299 at distance 108.224 which
is larger than the 1-4 table size 1.000 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
The parameters I use are the following:
title = PS
cpp = /lib/cpp
integrator = md
dt = 0.0001 ; ps !
nsteps = 10000 ; total 10 ps
nstlist = 10
nstxout = 100
nstvout = 100
nstenergy = 100
unconstrained-start = yes
nstxtcout = 50
nstlog = 50
constraints = none
ns_type = grid
vdwtype = Cut-off
fourierspacing = 0.055 ; Lbox/0.055 ~ 50
rlist = 0.9
rvdw = 1.2
tc_grps = system
tcoupl = berendsen
tau_t = 0.1
ref_t = 540
Pcoupl = no
optimize_fft = yes
the rest is set default
Did I miss something? What goes wrong?
You are running a very high temperature with no bond constraints. I would
expect you would need a very small timestep (like 0.1 fs) to get reasonable
dynamics. Try using constraints.
-Justin
Any help and/or comments are really appreciated.
Thank you!
Andrea
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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