From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Wed Oct 14 2009 - 23:09:36 CDT
details from namdlog file:
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL
TOTAL3 TEMPAVG PRESSURE GPRESSURE
VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 22603.2292 87823.3560 42797.7280
2560.8271 -860344.4192 3573.6873 0.0000
-1223.2033 201899.7757 -500309.0192 309.6828
-702208.7949 -498769.3330 309.6828 67.8086
90.4947 2851252.7895 67.8086 90.4947
..
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL
TOTAL3 TEMPAVG PRESSURE GPRESSURE
VOLUME PRESSAVG GPRESSAVG
ENERGY: 1700000 23299.3171 86391.1970 41722.6443
2532.5322 -667847.1747 40201.8371 0.0000
-4306686.9375 200963.7789 -4579422.8056 308.2472
-4780386.5845 -4577955.1526 309.4764 1.0066
1.0138 9999999999.9999 1.0132 1.0132
what is MISC energy?
On Wed, Oct 14, 2009 at 11:57 PM, Roman Petrenko <rpetrenko_at_gmail.com> wrote:
> Dear namd-ers,
> i simulated a protein system inserted in membrane in a water box with
> ions (total charge is close to zero) with PBC. Box size 159x159x112 A.
> NPT ensemble with electric field (of 1 namdconf unit) perpendicular to
> membrane was applied. Simulation runs normally up to 1,000,000 steps
> (2 ns) with normal decrease in total energy, temperature and pressures
> correspond to target values. Only slight increase in water box (by a
> couple of angstroms) was observed.
>
> Then, during the following 1.4 ns the box size increases to
> 5190x5190x3650 A and visually everything explodes.
>
> In other runs with exactly the same system but 10 times smaller
> electric field 4.4 ns of simulations are as expected.
>
> Should it explode when 10 ns is reached? Has anyone observed system
> explosion _after_ the system is minimized and partially equilibrated?
>
> --
> Roman Petrenko
> Physics Department
> University of Cincinnati
>
-- Roman Petrenko Physics Department University of Cincinnati
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