AMBER Archive (2008)

Subject: RE: AMBER: Whole System Equilibration & Pressure

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Apr 14 2008 - 16:37:51 CDT

Hi Deepa,

Pressure will always fluctuate by a lot - especially for a small system. See
what the moving average is for the pressure - that will let you see if there
is a trend there. Your average should ultimately come out as 1.0 (or
whatever you set pres0 to be) but it could take a long time to get there.
Plus will obviously be skewed by the initial portion of the simulation where
it was out of equilibrium. Hence why moving averages are useful. Try
calculating the average of the last 100ps of your trajectory.

You should also look take a look at potential energy - see if the potential
energy still has, for example, a downard drift towards the end of your
simulation.

In summary - don't worry about large fluctuations in the pressure. And for
checking averages check it over defined regions of your trajectory. E.g. if
the density should converge to exactly 1.0 but started off at 0.8 then an
average of the entire trajectory will only show it asymptotically converging
to 1.0 since the early data skews the average.

I hope that helps,

Good luck,
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of dpandit_at_brandeis.edu
> Sent: Monday, April 14, 2008 13:58
> To: amber_at_scripps.edu
> Subject: AMBER: Whole System Equilibration & Pressure
>
> Hi All:
> After conducting initial 20 PS (protein restrained 5
> kcal/mol.A2) constant volume equilibration for target temperature of
> 310K, I switched to 200 PS constant pressure (unrestrained - whole
> system) with pres0 = 1.0. Below are the details. When I checked the
> output, temperature and density looks reasonable but I am not sure
> about the pressure values as values fluctuate continuously. I have
> posted the selected values. Please let me know if I should
> post those
> values in detail. What should I do now? I am not sure what
> have I done
> wrong. Please help.
>
> THX
> Deepa
>
> Input File
>
> Stage 2 - Complete System Equilibration/Heating - 200ps MD
> &cntrl imin = 0,
> irest = 1,
> ntx = 7,
> ntb = 2,
> pres0 = 1.0,
> ntp = 1,
> taup = 2.0
> cut = 10,
> ntr = 0,
> ntc = 2,
> ntf = 2,
> tempi = 310.0
> temp0 = 310.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 100000,
> dt = 0.002,
> ntpr = 100, ntwx = 100, ntwr = 1000,
> /
>
>
> summary_avg.PRES summary_rms.PRES
>
> 220.000 -29.9 220.000 201.4
>
> summary_avg.VOLUME summary_rms.VOLUME
> 220.000 301709.6243 220.000 4746.6871
>
> summary_avg.DENSITY summary_rms.DENSITY
> 220.000 1.0059 220.000 0.0145
>
> summary_avg.TEMP summary_rms.TEMP
> 220.000 310.01 220.000 1.78
>
> Selected Pressure Values
>
> 216.000 -218.9
> 216.200 102.1
> 216.400 2.4
> 216.600 -168.3
> 216.800 -234.5
> 217.000 -310.6
> 217.200 -94.9
> 217.400 50.2
> 217.600 -232.0
> 217.800 -117.7
> 218.000 -205.4
> 218.200 -94.3
> 218.400 129.0
> 218.600 219.0
> 218.800 -271.1
> 219.000 45.4
> 219.200 47.9
> 219.400 65.4
> 219.600 -75.4
> 219.800 -121.2
> 220.000 193.0
>
> --------------------------------------------------------------
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