[gmx-users] Pressure coupling problem
Justin A. Lemkul
jalemkul at vt.edu
Mon Apr 11 23:17:59 CEST 2011
Fabian Casteblanco wrote:
> Hi,
>
> I'm still in my first few months of using Gromacs. I started by
> creating an *.itp and *.top file for /Ethanol/ using CHARMM force field
> parameters. I made the molecule and it looked fine, put 1000 molecules
> in a box, energy minimized it to a negative potential energy, viewed it
> on VMD, again looks fine. When I started running the NVT script, I set
> it equal to a ref_T of 298 K. It equilibrated at the temperature. Then
> I tried using an NPT script to equilibrate it to a ref_p of 1 bar. This
> is where I get the problem. The output shows the density is close to
> the actual experimental value of 0.789 g/cm^3. But for some reason, my
> pressure never gets an average of 1 bar. It keeps oscillating, which I
> understand is normal, but the average is always 1.3 or 1.4 bar (it seems
> the longer I let it run, the larger the average pressure; 1.38 for
> 50,000 steps,dt=0.002 and 1.45 for 75,000 steps,dt=0.002). I don't
> understand why the ref_p of 1 bar is not working when I run this NPT.mdp
> script file. My simple goal is to have 1000 molecules of ethanol using
> CHARMM ff parameters at 25degC and 1 bar and somewhere near the
> experimental density.
>
Your equilibration period (100-150 ps) is rather short, and the systematic
increase suggests that you're simply not equilibrated yet.
Also bear in mind that a quantity that is prone to pressure fluctuations in the
hundreds to thousands can only be so accurate. There was a very thorough
discussion about the statistical significance of pressure values that are not
equal to ref_p just some time ago. You may want to look through the archives to
find this discussion.
-Justin
> I would really appreciate anybody's help! I'm new to this but I'm eager
> to keep getting better.
>
> Thanks.
>
> _NVT SCRIPT (this works fine and takes me to 298 K)_
> File Edit Options Buffers Tools Help
> title =CHARMM ETHANOL NVT equilibration
> ;define =-DPOSRES ;position restrain the protein
> ;Run parameters
> integrator =md ;leap-frog algorithm
> nsteps =50000 ;2 * 50000 = 100 ps
> dt =0.002 ;2fs
> ;Output control
> nstxout =100 ;save coordinates every 0.2 ps
> nstvout =100 ;save velocities every 0.2 ps
> nstenergy =100 ;save energies every 0.2 ps
> nstlog =100 ;update log file every 0.2 ps
> ;Bond parameters
> continuation =no ;first dynamics run
> constraint_algorithm=lincs ;holonomic constraints
> constraints =all-bonds ;all bonds (even heavy atom-H
> bonds)constraind
> lincs_iter =1 ;accuracy of LINCS
> lincs_order =4 ;also related to accuracy
> ;Neighborhood searching
> ns_type =grid ;search neighboring grid cells
> nstlist =5 ;10 fs
> rlist =1.0 ;short-range neighborlist cutoff (in nm)
> rcoulomb =1.0 ;short-range electrostatic cutoff (in nm)
> rvdw =1.0 ;short-range van der Waals cutoff (in nm)
> ;Electrostatics
> coulombtype =PME ;Particle Mesh Ewald for long-range
> electrostat\
> ;ics
> pme_order =4 ;cubic interpolation
> fourierspacing =0.16 ;grid spacing for FFT
> ;Temperature coupling is on
> tcoupl =V-rescale ;modified Berendsen thermostat
> tc_grps =SYSTEM ;two coupling groups - more accurate
> tau_t =0.1 ;0.1 ;time constant, in ps
> ref_t =298 ;25 ;reference temperature, one
> for each \
> ;group, in K
> ;Pressure coupling is off
> pcoupl =no ;no pressure coupling in NVT
> ;Periodic boundary conditions
> pbc =xyz ; 3-D PBC
> ;Dispersion correction
> DispCorr =EnerPres ;account for cut-off vdW scheme
> ;Velocity generation
> gen_vel =yes ;assign velocities from Maxwell distribution
> gen_temp =25 ;temperature for Maxwell distribution
> gen_seed =-1 ;generate a random seed
> ;END
>
> _NPT SCRIPT_
> File Edit Options Buffers Tools Help
> title =Ethanol npt equilibration
> ;define =-DPOSRES ;position restrain the protein
> ;Run parameters
> integrator =md ;leap-frog algorithm
> nsteps =50000 ;2 * 50000 = 100 ps
> dt =0.002 ;2fs
> ;Output control
> nstxout =100 ;save coordinates every 0.2 ps
> nstvout =100 ;save velocities every 0.2 ps
> nstenergy =100 ;save energies every 0.2 ps
> nstlog =100 ;update log file every 0.2 ps
> ;Bond parameters
> continuation =yes ;Restarting after NVT
> constraint_algorithm=lincs ;holonomic constraints
> constraints =all-bonds ;all bonds (even heavy atom-H
> bonds)constraind
> lincs_iter =1 ;accuracy of LINCS
> lincs_order =4 ;also related to accuracy
> ;Neighborhood searching
> ns_type =grid ;search neighboring grid cells
> nstlist =5 ;10 fs
> rlist =1.0 ;short-range neighborlist cutoff (in nm)
> rcoulomb =1.0 ;short-range electrostatic cutoff (in nm)
> rvdw =1.0 ;short-range van der Waals cutoff (in nm)
> ;Electrostatics
> coulombtype =PME ;Particle Mesh Ewald for long-range
> electrostat\
> ;ics
> pme_order =4 ;cubic interpolation
> fourierspacing =0.16 ;grid spacing for FFT
> ;Temperature coupling is on
> tcoupl =V-rescale ;modified Berendsen thermostat
> tc-grps =SYSTEM ;two coupling groups - more accurate
> tau_t =0.1; 0.1 ;time constant, in ps
> ref_t =298; 300 ;reference temperature, one
> for each \
> ;group, in K
> ;Pressure coupling is on
> pcoupl =Parrinello-Rahman ;Pressure coupling on in NPT
> pcoupltype =isotropic ;uniform scaling of box vectors
> tau_p =2.0 ;time constant, in ps
> ref_p =1.0 ;reference pressure, in bar
> compressibility =4.5e-5 ;isothermal compressibility of h2O, 1/bar
> ;Periodic boundary conditions
> pbc =xyz ; 3-D PBC
> ;Dispersion correction
> DispCorr =EnerPres ;account for cut-off vdW scheme
> ;Velocity generation
> gen_vel =no ;Velocity generation is off
> ;gen_temp =25 ;temperature for Maxwell distribution
> ;gen_seed =-1 ;generate a random seed
> ;END
>
>
> --
> *Best regards,*
> **
> *Fabian F. Casteblanco*
> *Rutgers University -- *
> *Chemical Engineering PhD Student*
> *C: +908 917 0723*
> *E: **fabian.casteblanco at gmail.com* <mailto:fabian.casteblanco at gmail.com>
>
--
========================================
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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