[gmx-users] Inaccurate pressure readings
Denny Frost
dsfrost at cableone.net
Tue Feb 1 22:31:21 CET 2011
Here is the mdp file
title = HEX
cpp = /lib/cpp
constraints = hbonds
integrator = md
dt = 0.002 ; ps !
nsteps = 2500000 ; total 5ns.
nstcomm = 10
nstxout = 50000
nstvout = 50000
nstfout = 0
nstlog = 5000
nstenergy = 5000
nstxtcout = 25000
nstlist = 10
ns_type = grid
pbc = xyz
coulombtype = Cut-off
vdwtype = Cut-off
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl = v-rescale
tc_grps = HEX
tau_t = 0.1
ref_t = 300
nsttcouple = 1
; Energy monitoring
energygrps = HEX
; Isotropic pressure coupling is now on
Pcoupl = berendsen
pcoupltype = isotropic
;pc-grps = BMI PFF
tau_p = 1.0
ref_p = 1.0
compressibility = 4.5e-5
; Generate velocites is off at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 100000
This is the 'averages' section
" <=" ===== ######## ####### ==>
" <=" === A V E R A G E S ====>
" <=" = ############ ### ======>
" St" atistics over 1 0000001 steps u sing 10000001 f rames
Energies (kJ/mo l)
Bond Angle Ry ckaert-Bell. LJ (SR) Coulomb (SR)
4.57E+03 3.62E+03 3.34E+03 -2.08E+04 0.00E+00
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-9.28E+03 1.63E+04 7.05E+03 3.00E+02 9.96E+02
Box-X Box-Y Box-Z
5.47E+00 5.47E+00 5.47E+00
Total Virial (k J/mol)
5.44E+02 -1.30E-01 8.27E-02
-1.30E-01 5.44E+02 3.46E-02
8.27E-02 3.46E-02 5.44E+02
Pressure (bar)
9.96E+02 2.34E-02 -1.51E-02
2.34E-02 9.96E+02 -2.77E-02
-1.51E-02 -2.77E-02 9.96E+02
Total Dipole (D )
0.00E+00 0.00E+00 0.00E+00
I don't have an RMS section on my log file.
The final xvg file that comes from g_energy is much too long to post here,
but contains exactly what is in the log file. The interactive output from
g_energy is, however, thus:
Pressure = 995.9 bar (error = 0.65 bar)
On Tue, Feb 1, 2011 at 1:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Denny Frost wrote:
>
>> Sorry to revisit this subject, but this output does not make sense. In
>> the log file from my NPT simulation, the pressure readings fluctuate between
>> about 300 bar and -300 bar, which I gather is pretty normal. However, at
>> the end of the log file, it reports the average pressure being almost 1000
>> bar. g_energy also reports this value. In my mdp file, nstenergy is equal
>> to nstlog, so the frequency of data is the same in the .edr file. How is is
>> possible that the final average would be greater than any value obtained
>> during the simulation?
>>
>>
> As I recall from the previous discussion, there were lots of things wrong
> with your .mdp file and many things to troubleshoot. Can you please post:
>
> 1. The .mdp file you're using
> 2. The contents of the "AVERAGES" and "RMS FLUCTUATIONS" sections of your
> .log file
> 3. The g_energy output (not the header stuff, just the actual meaningful
> result)
>
> -Justin
>
> On Thu, Jan 20, 2011 at 4:33 PM, Mark Abraham <Mark.Abraham at anu.edu.au<mailto:
>> Mark.Abraham at anu.edu.au>> wrote:
>>
>> On 21/01/2011 10:12 AM, Denny Frost wrote:
>>
>>> Sorry, I'm referring to a lot of runs here - some fluctuate more
>>> than others and some have greater average values than others. The
>>> average value is never greater than the maximum fluctuation in
>>> each run, so that is not a problem. The average given by
>>> g_energy, however, is not close to 1.0 bar in any of my runs.
>>> Some runs give an average pressure of 10 bar, some give an
>>> average value of -1000 bar.
>>>
>>
>> In addition to all the points Justin mentioned, I'd observe that
>> you're generating velocities at the start of the run, so the system
>> will not be equilibrated for some time after that. See the advice
>> here
>> www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>> <
>> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>> >.
>>
>> Anyway, you don't want to collect data for averages until after
>> equilibration.
>>
>> Secondly, tau-t of 0.1 is useful for equilibration, but a bit too
>> stringent for actual simulations. Using v-rescale T-coupling is
>> probably a good idea too.
>>
>> Until you address all these issues about the numerical quality of
>> your model of reality, hoping for observables to correlate with
>> reality is not justified.
>>
>> Mark
>>
>>
>>
>>> On Thu, Jan 20, 2011 at 3:51 PM, Dallas Warren
>>> <Dallas.Warren at monash.edu <mailto:Dallas.Warren at monash.edu>> wrote:
>>>
>>> Then something you have said isn’t right. In first email you
>>> said that the pressure varies between -400 and +400 bar. Now
>>> you say that the average can vary from -1000 to +1000 bar. If
>>> the instantaneous pressure is varying from -1000 to +1000 bar,
>>> then that is not a real issue. However, if the average can be
>>> from -1000 to +1000 bar, then that definitely is.
>>>
>>>
>>> Which one is it?
>>>
>>>
>>> Catch ya,
>>>
>>> Dr. Dallas Warren
>>>
>>> Medicinal Chemistry and Drug Action
>>>
>>> Monash Institute of Pharmaceutical Sciences, Monash University
>>> 381 Royal Parade, Parkville VIC 3010
>>> dallas.warren at monash.edu <mailto:dallas.warren at monash.edu>
>>>
>>>
>>> +61 3 9903 9304
>>> ---------------------------------
>>> When the only tool you own is a hammer, every problem begins
>>> to resemble a nail.
>>>
>>>
>>> *From:* gmx-users-bounces at gromacs.org
>>> <mailto:gmx-users-bounces at gromacs.org>
>>> [mailto:gmx-users-bounces at gromacs.org
>>> <mailto:gmx-users-bounces at gromacs.org>] *On Behalf Of *Denny
>>> Frost
>>> *Sent:* Friday, 21 January 2011 9:23 AM
>>> *To:* Discussion list for GROMACS users
>>> *Subject:* Re: [gmx-users] Inaccurate pressure readings
>>>
>>>
>>> The average I calculate is not within -10 to 10, it is on the
>>> order of -1000 to 1000
>>>
>>> On Thu, Jan 20, 2011 at 3:11 PM, Dallas Warren
>>> <Dallas.Warren at monash.edu <mailto:Dallas.Warren at monash.edu>>
>>>
>>> wrote:
>>>
>>> You have a variable that is fluctuating over a range of 800+
>>> units (three orders of magnitude) and want the average to be 1.0?
>>>
>>>
>>> It is not a problem as such. If you can get a large enough
>>> data set of pressure data, and it will have to be very large,
>>> then you might get it close to one.
>>>
>>>
>>> But as long the average you calculate is within may be an
>>> order of magnitude (-10 to 10) then there is nothing to get
>>> too worried about.
>>>
>>>
>>> Catch ya,
>>>
>>> Dr. Dallas Warren
>>>
>>> Medicinal Chemistry and Drug Action
>>>
>>> Monash Institute of Pharmaceutical Sciences, Monash University
>>> 381 Royal Parade, Parkville VIC 3010
>>> dallas.warren at monash.edu <mailto:dallas.warren at monash.edu>
>>>
>>>
>>> +61 3 9903 9304
>>> ---------------------------------
>>> When the only tool you own is a hammer, every problem begins
>>> to resemble a nail.
>>>
>>>
>>> *From:* gmx-users-bounces at gromacs.org
>>> <mailto:gmx-users-bounces at gromacs.org>
>>> [mailto:gmx-users-bounces at gromacs.org
>>> <mailto:gmx-users-bounces at gromacs.org>] *On Behalf Of *Denny
>>> Frost
>>> *Sent:* Friday, 21 January 2011 9:07 AM
>>> *To:* gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>>>
>>> *Subject:* [gmx-users] Inaccurate pressure readings
>>>
>>>
>>> I am running a variety of NPT simulations with polar,
>>> non-polar, and ionic compounds. Although my results for
>>> density agree well with experimental values, the pressures I
>>> get from g_energy are off by 1 to 3 orders of magnitude. In
>>> the log file, the pressure fluctuates around a lot from -400
>>> to 400 bar, which seems to be normal according to other posts
>>> on this list, but the average (which is what g_energy gives
>>> me) is not 1.0 bar, as I specified. Does anyone know how to
>>> correct this problem?
>>>
>>>
>>> Pressure coupling parameters:
>>>
>>> Pcoupl = berendsen
>>>
>>> pcoupltype = isotropic
>>>
>>> tau_p = 1.0
>>>
>>> ref_p = 1.0
>>>
>>> compressibility = 4.5e-5
>>>
>>>
>>> --
>>>
>>>
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>>
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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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