[gmx-users] Pressure Fluctuations
Kavyashree M
hmkvsri at gmail.com
Wed Mar 16 17:06:44 CET 2011
Thank you Justin!
On Wed, Mar 16, 2011 at 9:28 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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 <jalemkul at vt.edu<mailto:
>> 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.
>>
>> -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.abraham at anu.edu.au <mailto:mark.abraham at anu.edu.au>
>> <mailto: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>
>> <mailto: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
>>
>> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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