Theres no density fluctuation it is constant at 1.02 -1.04.it seems stable
the rmsd variation is upto 3 Angstrom. I have minimized it well using SD CG
2500 & 1000.I did the equilibration using constant volume before switching
to constant pressure.I am just pasting the output file .Kindly have a look .
NSTEP = 1200 TIME(PS) = 197.400 TEMP(K) = 299.19 PRESS =
168.8
Etot = -97883.2983 EKtot = 20321.9742 EPtot =
-118205.2724
BOND = 632.6287 ANGLE = 1597.1408 DIHED =
2064.4037
1-4 NB = 722.3267 1-4 EEL = 7226.6508 VDWAALS =
18757.2432
EELEC = -149205.6663 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 9151.0404 VIRIAL = 7942.7748 VOLUME =
331516.9107
Density =
1.0234
Ewald error estimate: 0.6360E-04
------------------------------------------------------------------------------
NSTEP = 1400 TIME(PS) = 197.800 TEMP(K) = 298.86 PRESS =
-12.4
Etot = -97530.9767 EKtot = 20299.3874 EPtot =
-117830.3641
BOND = 608.6647 ANGLE = 1573.3435 DIHED =
2078.4009
1-4 NB = 713.2550 1-4 EEL = 7285.1817 VDWAALS =
18531.7813
EELEC = -148620.9911 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 8983.8472 VIRIAL = 9072.6985 VOLUME =
331496.3989
Density =
1.0235
Ewald error estimate: 0.1329E-04
------------------------------------------------------------------------------
NSTEP = 1600 TIME(PS) = 198.200 TEMP(K) = 299.33 PRESS =
-62.9
Etot = -97512.2395 EKtot = 20331.7675 EPtot =
-117844.0069
BOND = 578.9559 ANGLE = 1558.2519 DIHED =
2073.0667
1-4 NB = 726.7111 1-4 EEL = 7324.0603 VDWAALS =
18383.4961
EELEC = -148488.5489 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 9067.0310 VIRIAL = 9517.6439 VOLUME =
331607.7945
Density =
1.0231
Ewald error estimate: 0.1338E-03
As we see that pressure is fluctuating but volume is constant.
My input file is
Production of MD
&cntrl
imin=0,irest=1,
ntx=7,ntb=2,
ntp=1,pres0=1.0,
taup=2.0,
cut=10,
ntr=0,
ntc=2,ntf=2,
tempi=300.0,
temp0=300.0,
ntt=3,gamma_ln=1.0,
nstlim = 500000, dt = 0.002,
ntpr=200, ntwx=500, ntwr=1000
/
Thanks once again.
Regards
Ashutosh Shandilya
On 12 May 2010 11:34, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, May 12, 2010 at 1:59 AM, ashutosh shandilya
> <izerokelvin.gmail.com>wrote:
>
> > Hi All
> > 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.
> >
>
> >From what I understand, the density is a better gauge for this. What do
> the
> density fluctuations look like?
>
> Does your system appear stable when you look at it in a visualization
> program? If not, you may not have prepared your system carefully enough
> (i.e. minimized and equilibrated at constant volume).
>
> Beyond this, we would likely need more information to help diagnose any
> problem if it exists.
>
> All the best,
> Jason
>
>
> > Thanks in advance
> > Regards
> >
> > Ashutosh Shandilya
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 11 2010 - 23:30:04 PDT
