[gmx-users] pressure coupling

[Mark Abraham]

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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