[gmx-users] Pressure coupling problem
Fabian Casteblanco
fabian.casteblanco at gmail.com
Mon Apr 11 22:55:16 CEST 2011
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.
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* <fabian.casteblanco at gmail.com>
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