Kavyashree M wrote:
Thank you Justin,
When I went through most of the mailing list the fluctuations are not
so high
and even in the FAQ it was mentioned in the range of 500-600 bar for 216
water.
You cannot always assume that rules of thumb and others' results will (or
should) necessarily match your own. Unless you are using identical input files,
you won't necessarily get the same results. Much of the fluctuation information
is probably based on the Berendsen thermostat, which does not oscillate as much
as Parrinello-Rahman. Other factors in the .mdp file will influence these
statistics, since both the kinetic energy of the system and the virial are used
to calculate pressure (see the manual).
And more over the average pressure was ~6bar instead of 1bar which was
required.
And with fluctuations +/- 1000, is 6 really all that different from 1? There
was an extensive discussion some time back about this. I would suggest you have
a look through the archive.
So would you suggest that I can proceed with this file for the
production run without
any problem. I was following your lysozyme tutorial where fluctuations
were much
less.. hence I suspected some problem in this data.
The lysozyme system has nearly twice the number of waters that your system has
(over 10,000), hence the fluctuations will be much smaller, and even then, the
pressure oscillates by +/- 400 or so.
Again, I see no problem here. What you report is what is to be expected.
-Justin
Thanking you
With regards
M. Kavyashree
On Wed, Mar 16, 2011 at 8:52 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Kavyashree M wrote:
Thank you Sir
I am using OPLSAA with tip4p water model, I agree to the fact that
it will oscillate but the oscillation is this case was from
appr. -1000bar
to 1000bar. And as it is stated in the FAQ regarding the
variation of
fluctuations with number of waters, this system has 6882 waters
along
with a protein of 123 aa, so is not this fluctuations high?
No. It is entirely expected, as you've been told. Also pay
attention to this statement from the page linked before:
"How much it varies and the speed at which it does depends on the
type of pressure coupling used and the value of the coupling constants."
You may not see the exact same behavior described on the Pressure
page if you're using different settings.
There is no problem here.
-Justin
Pressure coupling used -parinello-rahman
tau_p = 2.0
tau_t = 1.0
compressibility 4.5e-5
Pcouple_type = isotropic
Any suggestions?
Thanking you
With Regards
M. Kavyashree
On Wed, Mar 16, 2011 at 12:10 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>> wrote:
On 16/03/11, *Kavyashree M * <hmkv...@gmail.com
<mailto:hmkv...@gmail.com>
<mailto:hmkv...@gmail.com <mailto:hmkv...@gmail.com>>> wrote:
Dear users,
Upon was trying to simulate an npt ensemble (protein in
water),
pressure was coupled using parinello rahman system with
tau_p = 2,
tau_t = 1; compressibility 4.5e-5, type = isotropic.
(cut off scheme (vdw_type = switch; rvdw = 1.0;
rvdw_switch = 0.9;
rcoulomb = 1.2; rlist = 1.2).
No matter what value of tau_p is used (0.5, 1, 2, 2.5, 3,
3.5),
the pressure
fluctuations are very drastic. I have gone through the
mailing
list regarding
this issue but could not come to any conclusion.
Any suggestions are helpfull.
This is one of the statistics for pressure fluctuations.
Statistics over 500001 steps [ 0.0000 through 1000.0000
ps ], 1
data sets
All statistics are over 100001 points
Energy Average Err.Est. RMSD
Tot-Drift
-------------------------------------------------------------------------------
Pressure 5.77629 0.99 398.013
-5.34218 (bar)
Looks very normal. See http://www.gromacs.org/Documentation/FAQs
number 3
Mark
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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