[gmx-users] Negative average pressure value after NPT equilibration
Dario Akaberi
dario.aka17 at gmail.com
Sun Oct 23 16:54:45 CEST 2016
I forgot to say that after 500ps of NPT equilibration the density was:
Average Err.Est. RMSD Tot-Drift
Density 1009.3 0.1 3.09051 0.471894
(kg/m^3)
On Sun, Oct 23, 2016 at 4:07 PM, Dario Akaberi <dario.aka17 at gmail.com>
wrote:
> 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/Documen
>> tation/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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