normal problem with pressure

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9 years 5 months ago #4127 by initram
problem with pressure was created by initram
Hi,

I am using standard .mdp file from download page with Berendsen p and T coupling.
If I first perform NVT equilibration I see holes in the system, If I skip NVT equilibration and I only do NPT equilibration my temperature is correct but my pressure is low (~0.4 bar instead of 1.0 bar).

Any suggestions what went wrong?

Thanks

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9 years 5 months ago #4128 by xavier
Replied by xavier on topic problem with pressure
Depending on how you build your system a non-equilibrated NVT ensemble might indeed not be appropriate and if the box size on the x/y dimensions are not correct you will see holes forming or a gel phase.

P=0.4 might simply reflect a short simulation. The pressure takes some time to equilibrate and you need to simulate long enough to get a meaningful average.

initram wrote: Hi,

I am using standard .mdp file from download page with Berendsen p and T coupling.
If I first perform NVT equilibration I see holes in the system, If I skip NVT equilibration and I only do NPT equilibration my temperature is correct but my pressure is low (~0.4 bar instead of 1.0 bar).

Any suggestions what went wrong?

Thanks

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9 years 3 weeks ago #4479 by initram
Replied by initram on topic problem with pressure
Hi Xavier,

I extended simulation and now everything is OK.
Actually, just subtracting first ~100 steps gave me correct pressure.

Thank you again

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