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 <[email protected]
<mailto:[email protected]>> wrote:
On 16/03/11, *Kavyashree M * <[email protected]
<mailto:[email protected]>> 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
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
