[gmx-users] possible bug in posre

[Sergio Manzetti]

Hi, I have made 5 copies of a simulation, using the following mdp , with gen-seed = 17529, 17528, 17527, 17526 and 17525. In this simulation, thre is a piece of DNA; with posre etc. In simulation one, after 20 ns, the DNA is bound to some other molecule and everything looks OK. In simulation 2, 3, 4 and 5 the DNA strands fly everywhere in the box, outside the box and even double up in longitude direction. All the directories are identical in their files, and the grompp has been used respectively. Does this sound familiar to some, or is it most likely a grompp error? This is the second time I try this. 


title = DNA in water stabilization 
cpp = /lib/cpp 
include = -I../top 
define = 
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 = 17529 
constraints = all-bonds 



Sergio Manzetti 

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