Dear Sergio,
how did you define the position restrain in your topology? Check your
topology and position restrain file.
All the best
Johannes
On 07.09.2017 11:07, Sergio Manzetti wrote:
Hello, I am running 5 simulations with the given mdp:
title = DNA in water stabilization
cpp = /lib/cpp
include = -I../top
define = -DPOSRES
integrator = md
dt = 0.002
nsteps = 10000000
nstxout = 5000
nstvout = 5000
nstlog = 5000
nstenergy = 300
nstxout-compressed = 300
compressed-x-grps = PRB SOL NA CL DNA
energygrps = PRB SOL NA CL DNA
nstlist = 10
ns-type = grid
rlist = 0.8
coulombtype = PME
rcoulomb = 0.8
rvdw = 0.8
tcoupl = V-Rescale
tc-grps = System
tau-t = 0.1
ref-t = 310
Pcoupl = No
tau-p = 1.0
compressibility = 4.5e-5
ref-p = 1.0
gen-vel = yes
gen-temp = 310
gen-seed = 17527
constraints = all-bonds
and still, the DNA splits into two....
Any ideas what could be wrong?
Thanks
Sergio Manzetti
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