On 17/12/2011 4:58 PM, mohammad agha wrote:
Dear GROMACS Users
I have a warning after doing pr.mdp as followed, I read errors in
GROMACS site and checked mailing list, but my warning is only step1
and after that equilibration is run normally till end.
5000000 steps, 150000.0 ps.
step 0
Step 1 Warning: pressure scaling more than 1%, mu: 1.04679 1.04679
1.04679
Step 1 Warning: pressure scaling more than 1%, mu: 1.04679 1.04679
1.04679
my pr.mdp about pressure coupling is:
pcoupl = berendsen
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 4 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ;isothermal compressibility of water, bar^-1
I work in Martini Coarse-Grained and my time step is 0.03 ps. I
increased tau_p but my warning increased to step 1 and step 11, I
think this warning since it is only in initial steps isn't important,
is my idea right?
That kind of thing is normal in the very early stages of NPT
equilibration when the volume is not quite right. mdrun is just warning
you that there are some changes going on. Use g_energy to see those. If
it bothers you, then you will want to adjust your density (i.e. number
of water molecules) before starting.
Mark
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