[gmx-users] Pressure coupling and cut-off

[Justin A. Lemkul]

Yanmei Song wrote:
> Dear Justin:
> 
> Thanks for your response. Here is the complete my .mdp file:
> 
> title               =  pdm
> cpp                 =  /lib/cpp
> constraints         =  all_bonds
> integrator          =  md
> dt                  =  0.004   ; ps !
> nsteps              =  2500000   ; total 10ns.
> nstcomm             =  1
> nstxout             =  50000
> nstvout             =  50000
> nstfout             =  0
> nstlog              =  5000
> nstenergy           =  5000
> nstxtcout           =  25000
> nstlist             =  10
> ns_type             =  grid
> pbc                 =  xyz
> coulombtype         =  PME
> rlist               =  1.4
> rcoulomb            =  1.4
> rvdw                =  1.4
> fourierspacing      =  0.20
> pme_order           =  4
> ewald_rtol          =  1e-5
> ; Berendsen temperature coupling is on in one groups
> Tcoupl              =  berendsen
> tc_grps             =  PDM
> tau_t               =  0.1
> ref_t               =  300
> ; Energy monitoring
> energygrps          =  PDM
> ; Isotropic pressure coupling is now on
> Pcoupl              =  berendsen
> pcoupltype          =  isotropic
> ;pc-grps            =  PDM
> 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
> 
> 

The problem you're seeing could be an artifact of the shorter cutoff.  Have you 
tried using DispCorr = EnerPres?  Or what about using a Shift function for 
vdwtype?  You might see better energy conservation in that case compared to a 
plain cutoff.

-Justin

> 
> On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Yanmei Song wrote:
> 
>         Dear All:
> 
>         I have question about the pressure coupling. I have done a 10ns
>         simulation with 19800 atoms for 120 large molecules using the
>         following pressure coupling.
> 
>         Tcoupl              =  berendsen
>         tc_grps             =  PDM
>         tau_t               =  0.1
>         ref_t               =  300
> 
>         Pcoupl              =  berendsen
>         pcoupltype          =  isotropic
>         ;pc-grps            =  PDM
>         tau_p               =  1.0
>         ref_p               =  1.0
>         compressibility     =  4.5e-5
> 
>         Then I did g_energy for the last 3ns and got the results:
> 
>         Energy                      Average       RMSD     Fluct.    
>          Drift  Tot-Drift
>         -------------------------------------------------------------------------------
>         Potential                    -98061          0          0  
>          0.61668    1850.04
>         Temperature                 303.561    109.602    109.602
>         0.000181791   0.545372
>         Pressure (bar)               4.4884    11110.8    11109.8
>          -0.169835   -509.506
> 
>         For such a long run the pressure drift is still too much and
>         seem hasn't approached 1bar. Does it mean the system hasn't
>         reach equilibrium yet. I did a similar system by using the same
>         method. it just take 2 or 3ns to reach the equilibrium. and the
>         pressure is around 1.01after the run. The only difference is the
>         cutoff changing from 1.2 to 1.4.  Does the cufoff of 1.4 is too
>         large to make the system running slower. Or the pressure
>         coupling method is not working well.  Anyone can give me any
>         suggestions?
> 
> 
> 
>     I think it will depend on the interplay of other parameters as well.
>      Posting a complete .mdp file may be more helpful.
> 
>     -Justin
> 
>         -- 
>         Yanmei Song
>         Ph.D. Candidate
>         Department of Chemical Engineering
>         Arizona State University
> 
> 
>         ------------------------------------------------------------------------
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     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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> 
> 
> 
> -- 
> Yanmei Song
> Ph.D. Candidate
> Department of Chemical Engineering
> Arizona State University

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================