[gmx-users] Negative average pressure value after NPT equilibration
Dario Akaberi
dario.aka17 at gmail.com
Sun Oct 23 16:07:29 CEST 2016
So In my system I had 1 protein and a second smaller protein associated to
it. Since the second protein was not even complete, I eliminated it from
the original PDB file I used to create the topology with pdb2gmx. I then
repeated the whole process and now my average pressure after 500 ps of NPT
equilibration is -3.31 with an Err. Est of 2.5, RMSD of 166.905, total
drift -6.63.
Is there anything I can do to get to the proper reference value of 1 bar? I
tried a 1ns NPT equilibration which resulted in an average pressure of
-4.77 and Err. EST of 3.8. So a longer equilibration is not gonna work In
my opinion.
On Sat, Oct 22, 2016 at 2:05 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> Negative pressure means the system wants to contract. But your simulations
> are probably too short to get a reliable measurement of pressure, nor to
> equilibrate it if you were not already very close to the right density. See
> background at e.g. http://www.gromacs.org/Documentation/Terminology/
> Pressure
> and
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tutorials/lysozyme/07_equil2.html
>
>
> Mark
>
> On Sat, Oct 22, 2016 at 1:34 PM Dario Akaberi <dario.aka17 at gmail.com>
> wrote:
>
> > Dear users
> >
> > I am trying to perform the MD simulation of a protein in water using the
> > amberFF99sb-ildn force field.
> >
> > To so so I created the protein topology specifying TIP3P water. then I
> > created a dodecahedron box with -d 1.0, I filled it using spc216.gro. and
> > added 7 NA ions. This resulted in a system of 8837 water molecules plus
> > the 7 ions and the protein. Minimization were carried out using conjugate
> > gradient method (gromacs is compiled with double precision) which
> converged
> > to emtol 0.01 in 48000 steps.The following nvt ensemble worked well (I
> > think) and the resulting average temperature was 299.702 (ref temperature
> > was 300 K) with Err. Est. = 0.32 RMSD 4.39922 and tot-Drift 1.58106.
> > Now the problems begin. After NVT equilibration I performed an NPT
> > equilibration step of 100 ps which resulted in an average pressure of
> -50.
> > I then tried to equilibrate for a longer time: 150 and 200 ps with the
> same
> > result. I also tried a 500 ps NPT equilibration which resulted in an
> > average pressure of -60 and average density 998.935 with Err. Est =
> 0.12,
> > RMSD = 2.38 and Tot-Drift = 0.83 /kg/m^3).
> >
> > This is the NPT.mdp file I used:
> >
> > define = -DPOSRES
> > integrator = md ; leap-frog integrator
> > nsteps = 50000 ; 2 * 50000 = 100 ps
> > dt = 0.002 ; 2 fs
> >
> > nstxout = 500 ; save coordinates every 1.0 ps
> > nstvout = 500 ; save velocities every 1.0 ps
> > nstenergy = 500 ; save energies every 1.0 ps
> > nstlog = 500 ; update log file every 1.0 ps
> >
> > continuation = yes ; Restarting after NVT
> > constraint_algorithm = lincs ; holonomic constraints
> > constraints = all-bonds ; all bonds (even heavy
> > atom-H bonds) constrained
> > lincs_iter = 1 ; accuracy of LINCS
> > lincs_order = 4 ; also related to accuracy
> >
> > cutoff-scheme = Verlet
> > ns_type = grid
> > nstlist = 10
> > rlist = 1.0
> > rcoulomb = 1.0
> > rvdw = 1.0
> >
> > coulombtype = PME
> > pme_order = 4
> > fourierspacing = 0.16
> >
> > ; Temperature coupling is on
> > tcoupl = V-rescale ; modified Berendsen
> > thermostat
> > tc-grps = Protein Non-Protein
> > tau_t = 0.1 0.1
> > ref_t = 300 300 ; reference
> > temperature, one for each group, in K
> >
> > 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 water, bar^-1
> > refcoord_scaling = com * I get an
> error
> > without this
> >
> > ; 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
> >
> > I don't know what I'm doing wrong, and unfortunately, I am new to
> molecular
> > dynamics simulation which doesn't help. I tried to find a solution and
> > found some other cases where people had a negative pressure after NPT
> > equilibration step but it was like an average pressure of -2 not -60!
> > Any help would be very appreciated.
> >
> > Thanks,
> >
> > Dario
> > --
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