Sir
Thanks a lot for all the required information .
I have plotted the density vs time graph which seems reasonably stable
which is with the attachment but still the average pressure is not close to
1.0. I am sending some steps of MD production.Kindly have a look and guide
me.
NSTEP = 499800 TIME(PS) = 2108.600 TEMP(K) = 298.22 PRESS =
-103.9
Etot = -97909.2164 EKtot = 20256.2925 EPtot =
-118165.5089
BOND = 599.4629 ANGLE = 1496.5131 DIHED =
2035.9336
1-4 NB = 724.9229 1-4 EEL = 7371.2412 VDWAALS =
18512.0359
EELEC = -148905.6186 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 8989.3901 VIRIAL = 9731.8551 VOLUME =
331039.8532
Density =
1.0249
Ewald error estimate: 0.2055E-03
------------------------------------------------------------------------------
NSTEP = 500000 TIME(PS) = 2109.000 TEMP(K) = 301.03 PRESS =
74.7
Etot = -97660.3242 EKtot = 20447.2482 EPtot =
-118107.5723
BOND = 627.9132 ANGLE = 1509.0913 DIHED =
2048.0135
1-4 NB = 714.7414 1-4 EEL = 7378.8329 VDWAALS =
18547.1983
EELEC = -148933.3628 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 9045.0106 VIRIAL = 8510.8363 VOLUME =
330974.6955
Density =
1.0251
Ewald error estimate: 0.5210E-04
------------------------------------------------------------------------------
A V E R A G E S O V E R 2500 S T E P S
NSTEP = 500000 TIME(PS) = 2109.000 TEMP(K) = 300.05 PRESS =
0.2
Etot = -97729.5356 EKtot = 20380.1791 EPtot =
-118109.7147
BOND = 611.6009 ANGLE = 1535.4058 DIHED =
2040.6715
1-4 NB = 728.7700 1-4 EEL = 7348.3174 VDWAALS =
18494.9129
EELEC = -148869.3933 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 9065.8209 VIRIAL = 9064.4785 VOLUME =
330848.0085
Density =
1.0255
Ewald error estimate: 0.8173E-04
------------------------------------------------------------------------------
Thanks once again.
Regards
Ashutosh Shandilya
On 12 May 2010 19:55, Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Ashutosh,
>
> > To run the constant pressure MD I used ntb=2,ntp=1,and taup=2 but when
> > plotted the graph for pressure it is varying large .Sometimes its going
> > negative what does this imply.
>
> This is perfectly normal. The instantaneous pressure will always fluctuate
> by large amounts. Negative pressures are also reasonable, they just imply
> that the box size needs to shrink slightly. Note with taup=2.0 this implies
> a 2ps relaxation time so the pressure will not be instantly readjusted to
> 1.0 on every step but instead will be adjusted such that it would reach
> this
> value after 2ps.
>
> Try looking at the average pressure. This should be close to 1.0.
>
> Also look at the density vs time, this will give you a more relevant plot
> to
> whether things are stable.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
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Received on Thu May 13 2010 - 00:30:06 PDT
