[gmx-users] Inaccurate pressure readings

[Denny Frost]

Sorry about forgetting the simulation time.  They run for about 12 ns, at
which point I stop them.  They appear stable - the box vectors don't change
a lot (which is surprising since the pressure sure does).  Below is a
complete mdp file.

title                 = Run1
cpp                 =  /lib/cpp
constraints         =  all_bonds
integrator          =  md
dt                  =  0.004   ; ps !
nsteps              =  20000000   ; total 4ns.
nstcomm             =  1
nstxout             =  50000
nstvout             =  50000
nstfout             =  0
nstlog              =  5000
nstenergy           =  5000
nstxtcout           =  25000
nstlist             =  10
ns_type             =  grid
pbc                 =  xyz
coulombtype         =  PME
vdwtype             =  Shift
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
fourierspacing      =  0.6
;pme_order           =  4
ewald_rtol          =  1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc_grps             =  BMI      PF6
tau_t               =  0.1  0.1
ref_t               =  300  300
nsttcouple          =  1
; Energy monitoring
energygrps          =  BMI      PF6
; 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


On Thu, Jan 20, 2011 at 3:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Denny Frost wrote:
>
>> from -1000 to 1000, depending on the system.  The simulation box is 8x8x8
>> nm (roughly) and contains about 12,000 atoms
>>
>>
> Are the systems even stable?  Is there a trend in the pressure, or is it
> stable at those values?  It seems that the systems are either exploding or
> imploding. How long are the simulations?  Can you post a complete .mdp file?
>
> -Justin
>
>  On Thu, Jan 20, 2011 at 3:09 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Denny Frost wrote:
>>
>>        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?
>>
>>
>>    What is the average value you're getting?  How long are your
>>    simulations?
>>
>>    -Justin
>>
>>
>>        Pressure coupling parameters:
>>        Pcoupl              =  berendsen
>>        pcoupltype          =  isotropic
>>        tau_p                   =  1.0
>>        ref_p                   =  1.0
>>        compressibility     =  4.5e-5
>>
>>
>>    --     ========================================
>>
>>    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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