Hello,
On Thu, Jun 24, 2010 at 6:28 AM, Ashutosh Shandilya
<izerokelvin.gmail.com>wrote:
> 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
>
Right here, the kinetic energy is certainly not zero. Again, these are
AVERAGES, since you did not print out any values between the start and end
(you print output every 2500 steps, with ntpr=2500, but you only run 2500
steps total).
> 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
>
These are RMS fluctuations (see the above title). At 10 K, I would expect
very few fluctuations, since a system so cold won't be able to move that
much (and you didn't give it a very long simulation).
> 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
>
The kinetic energy is still not zero here, though it's higher for sure.
This is to be expected since the temperature is 274.17 instead of 10, so
there should be much more kinetic energy.
> 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
>
> ------------------------------------------------------------------------------
>
Look after heating to higher temperatures. When you heat from 250 to 255,
I'm guessing you'll see some non-zero fluctuations. However, when running
at such low temperatures for so few steps, the fact that your values don't
fluctuate at all is unsurprising. Again, bear in mind that the zeroes
you're seeing are fluctuations, not actual values.
Hope this helps,
Jason
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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jun 24 2010 - 06:00:04 PDT
