[gmx-users] Pressure Fluctuations
hmkvsri at gmail.com
Wed Mar 16 16:43:51 CET 2011
Thank you Justin,
When I went through most of the mailing list the fluctuations are not so
and even in the FAQ it was mentioned in the range of 500-600 bar for 216
And more over the average pressure was ~6bar instead of 1bar which was
So would you suggest that I can proceed with this file for the production
any problem. I was following your lysozyme tutorial where fluctuations were
less.. hence I suspected some problem in this data.
On Wed, Mar 16, 2011 at 8:52 PM, Justin A. Lemkul <jalemkul at 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.
> 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.abraham at anu.edu.au<mailto:
>> mark.abraham at anu.edu.au>> wrote:
>> On 16/03/11, *Kavyashree M * <hmkvsri at gmail.com
>> <mailto:hmkvsri at 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
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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