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problem with pressure
- initram
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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
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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- xavier
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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.
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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- initram
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9 years 1 month 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
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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