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.castebla...@gmail.com* <mailto:fabian.castebla...@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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