Dear Amber users,
I am simulating (NPT) a protein-DNA complex in a truncated octahedron
box (*total
atoms: 50281*) under NPT condition, using *pmemd.mpi* utility of Amber12.
Total 50 restarts (each comprises of 10,00000 steps) was given. In each
restart.out file output was written after 2500 steps and averaging was done
on total 400 output steps.
The NPT simulation script file is :
-----------------------------------------------------------
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 8.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0, ig = -1, iwrap = 1,
nstlim = 1000000, dt = 0.002, nmropt =1,
ntpr = 2500, ntwx = 2500, ntwr = 2500,
ntwv = 2500, ntwe = 2500
/
&wt type='DUMPFREQ', istep1=2000
/
&wt type='END'
/
LISTOUT=POUT
DISANG=DIST.rst
DUMPAVE=rest_values_INPRORUN1
END
-----------------------------------------------------------
I have found surprising average pressure in some of the restart.out file
and they are as high as 15.00 bar, though the average density is ~1.00, the
output files are as follows:
*Output for average pressure after completion of every restart:*
---------------------------------------------------------------------------------------------------
NSTEP = 1000000 TIME(PS) = 2220.000 TEMP(K) = 299.93 PRESS =
1.0
*NSTEP = 1000000 TIME(PS) = 4220.000 TEMP(K) = 299.88 PRESS =
-15.9*
* NSTEP = 1000000 TIME(PS) = 6220.000 TEMP(K) = 299.96 PRESS
= 8.9*
NSTEP = 1000000 TIME(PS) = 8220.000 TEMP(K) = 299.99 PRESS =
4.9
NSTEP = 1000000 TIME(PS) = 10220.000 TEMP(K) = 300.06 PRESS =
-1.9
NSTEP = 1000000 TIME(PS) = 12220.000 TEMP(K) = 299.99 PRESS =
-4.4
NSTEP = 1000000 TIME(PS) = 14220.000 TEMP(K) = 299.85 PRESS =
0.4
NSTEP = 1000000 TIME(PS) = 16220.000 TEMP(K) = 299.95 PRESS =
2.8
NSTEP = 1000000 TIME(PS) = 18220.000 TEMP(K) = 299.93 PRESS =
-2.8
NSTEP = 1000000 TIME(PS) = 20220.000 TEMP(K) = 299.98 PRESS =
-3.7
NSTEP = 1000000 TIME(PS) = 22220.000 TEMP(K) = 300.06 PRESS =
0.7
NSTEP = 1000000 TIME(PS) = 24220.000 TEMP(K) = 299.98 PRESS =
1.6
* NSTEP = 1000000 TIME(PS) = 26220.000 TEMP(K) = 299.95 PRESS =
15.5*
NSTEP = 1000000 TIME(PS) = 28220.000 TEMP(K) = 300.14 PRESS =
1.6
Output for average Density
------------------------------------------
Density = 1.0147
Density = 1.0148
Density = 1.0146
Density = 1.0148
Density = 1.0148
Density = 1.0149
Density = 1.0148
Density = 1.0146
Density = 1.0148
---------------------------------------------------------------------------------------------
I have gone through three of your posts, where it is stated that due to the
small isothermal compressibility of liquid this happens. But my question is
can it be as high as 15.00 bar?
looking forward for your reply
Aditya
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Received on Sun Feb 15 2015 - 00:30:03 PST
