[gmx-users] Inaccurate pressure readings

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 21 00:00:26 CET 2011



Denny Frost wrote:
> 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.
> 

If the box vectors aren't changing, then it's very odd that the pressure is not 
a more acceptable value.  What of the other parameters - temperature, energy, 
etc?  What type of energy minimization and/or equilibration did you do prior to 
this run?

A few other notes:

> title                 = Run1
> cpp                 =  /lib/cpp
> constraints         =  all_bonds
> integrator          =  md
> dt                  =  0.004   ; ps !

Are you using virtual sites?  If not, a 4-fs timestep may not be stable, even 
with constraints.

> 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

This fourierspacing is 5-6 times larger than what is generally considered 
sufficiently accurate.  Your PME term may be inaccurate if there are 
insufficient grid points.  If you're increasing the spacing for performance 
reasons, you may be sacrificing accuracy.

> ;pme_order           =  4
> ewald_rtol          =  1e-5
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc_grps             =  BMI      PF6  

Are both of these groups large enough to warrant their own temperature coupling 
groups?

http://www.gromacs.org/Documentation/Terminology/Thermostats

-Justin

> 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 
> <mailto: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>
>         <mailto: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> <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 <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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