My question is bit confusing but please have a look.
At firstI am slowly heating the protein by 5 kelvin each for 2.5ps till 300K
and then equilibrating it for 1 ns.
My input during heating is
2.5ps MD equilibration on protein
&cntrl
imin = 0,
irest = 0,
ntx=1,
ntb=1,
cut = 10,
tempi = 0.0,
temp0 = 5.0,
ntt = 3,
nstlim = 2500, dt = 0.001,
ntpr = 2500, ntwx = 2500, ntwr = 2500
/
But the kinetic energy is showing zero.
A V E R A G E S O V E R 1 S T E P S
NSTEP = 2500 TIME(PS) = 150.000 TEMP(K) = 72.83 PRESS =
0.0
Etot = -169111.4515 EKtot = 8255.9104 EPtot =
-177367.3619
BOND = 24104.3780 ANGLE = 802.7751 DIHED =
1657.4515
1-4 NB = 523.7214 1-4 EEL = 5786.1030 VDWAALS =
45238.3168
EELEC = -255480.1077 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.2838E-03
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 2500 TIME(PS) = 150.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.0000E+00
------------------------------------------------------------------------------
during the equilibration my initial ouput is
200ps MD equilibration on protein
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2,
ntp=1,
taup=5.0,
cut = 10,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 200000, dt = 0.001,
I am getting this output and kinetic energy not zero here
NSTEP = 2500 TIME(PS) = 152.500 TEMP(K) = 274.17 PRESS =
-840.6
Etot = -117506.9692 EKtot = 21092.5993 EPtot =
-138599.5685
BOND = 529.1427 ANGLE = 1417.3676 DIHED =
1820.7304
1-4 NB = 576.3686 1-4 EEL = 5810.0334 VDWAALS =
25525.6428
EELEC = -174278.8539 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 9539.7005 VIRIAL = 17429.6705 VOLUME =
434711.0759
Density =
0.8851
Ewald error estimate: 0.1452E-03
------------------------------------------------------------------------------
NSTEP = 5000 TIME(PS) = 155.000 TEMP(K) = 293.01 PRESS =
-1051.4
Etot = -112394.8154 EKtot = 22541.8474 EPtot =
-134936.6629
BOND = 562.8501 ANGLE = 1489.2243 DIHED =
1872.2870
1-4 NB = 589.4253 1-4 EEL = 5808.5192 VDWAALS =
23161.4049
EELEC = -168420.3736 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 10169.9533 VIRIAL = 19831.1489 VOLUME =
425598.8833
Density =
0.9041
Ewald error estimate: 0.2519E-05
------------------------------------------------------------------------------
and the final ouput after equilibration is
A V E R A G E S O V E R 80 S T E P S
NSTEP = 200000 TIME(PS) = 350.000 TEMP(K) = 299.48 PRESS =
-59.7
Etot = -334568.4269 EKtot = 65433.1965 EPtot =
-400001.6234
BOND = 472.1758 ANGLE = 1253.0974 DIHED =
1652.0880
1-4 NB = 552.6828 1-4 EEL = 5450.3988 VDWAALS =
71535.7481
EELEC = -480917.8142 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 31822.7429 VIRIAL = 33304.2210 VOLUME =
1098956.9106
Density =
0.9966
Ewald error estimate: 0.6994E-04
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 200000 TIME(PS) = 350.000 TEMP(K) = 3.20 PRESS =
186.1
Etot = 2208.2715 EKtot = 698.9312 EPtot =
1550.7168
BOND = 20.8662 ANGLE = 28.8090 DIHED =
23.0102
1-4 NB = 9.6942 1-4 EEL = 29.6323 VDWAALS =
1159.0335
EELEC = 2655.0790 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 376.7829 VIRIAL = 4496.5090 VOLUME =
19622.8863
Density =
0.0166
Ewald error estimate: 0.4818E-04
------------------------------------------------------------------------------
Why after heating it is showing Zeroes and whats the effect.I am running
everything at constant pressure as from the values we see
constant volume not the constant pressure but the density plot is constant.
There are no zero values for Kinetic energy and all. Is there something
wrong and where I am going wrong.If any other files are require
please let me know. And I am still not sure of the constant pressure
although it was explained earlier.
Thanks in advance.
Ashutosh Shandilya
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Received on Thu Jun 24 2010 - 03:30:05 PDT
