[gmx-users] Use NVT to mimic NVE
Dr. Vitaly Chaban
vvchaban at gmail.com
Sun Oct 12 08:53:50 CEST 2014
Thus, what is your question now? :-)
The total energy must remain conserved at all times. That's it.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sun, Oct 12, 2014 at 2:45 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
> I tried PME and then potential-shift-verlet for Van der Waals. The energy
> is still not constant in mixed precision gromacs 5.0.1 NVE run on 12 xeon
> cpu without gpu. Those were nearly the last few things that I knew that I
> can try in mixed precision. The system has ~165 amino acid, ~9000 water,
> and 3 Cl- ion in a truncated rhombic dodecahedron box. Total energy of the
> following simulation drift constantly down. This production run was a
> continuation of ~300ns npt and ~300ns nvt. The PME grid was 80x80x80.
>
> ; Run parameters
> integrator = md-vv ; leap-frog integrator
> nsteps = 150000000 ; 1 ns
> dt = 0.0005 ; 0.5 fs
>
> ;NVE
> ; nstcomm = 500 ; remove center of mass motion to reduce energy and
> temp. drift. (seems less drift without this)
> shake-tol = 0.000001 ; shake tolerance.
> verlet-buffer-tolerance = 0.00000005
>
> ;Output control
> nstenergy = 20 ; save energies every 1.0 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)
> constrained
> lincs_iter = 2 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cells
> nstlist = 5 ; 10 fs
>
> vdw-modifier = Potential-shift-Verlet;
>
> rlist = 1.1 ; 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
> electrostatics
> pme_order = 6 ; cubic interpolation
> fourierspacing = 0.1 ; grid spacing for FFT
>
> ; Temperature coupling is off
> tcoupl = no ; modified Berendsen thermostat
> ; Pressure coupling is off
> pcoupl = no
>
> refcoord_scaling = com
> ; 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
> cutoff-scheme = Verlet
>
>
> I guess the energy leakage when no thermostat is used doesn't mean the
> distribution of conformation is incorrect when a thermostat is used.
> Since double precision run is stable while single precision is not, the
> energy leakage is caused by numerical error of the computer operation and
> algorithm instead of the physics or conformation of the setup. (only the
> precision changed. the mdp files were the same.)
>
> I also guess that the majority of simulations in published paper would have
> such constant drop/rise of total energy if the thermostat is switched off.
> ( Is this true??? )
>
> When the Amber99ff-ILDN force field is made, NPT and NVT is used, instead
> of NVE [http://dx.doi.org/10.1002%2Fprot.22711]
>
> The Amber lipid 14 forcefield uses NPT to create the parameters. In one of
> the validations, they ran NPT followed by NVE to calculate diffusion
> coefficient. The tolerance was more stringent in the NVE part than the NPT
> part. The plot of energy v.s. time seems to be not in the paper. [
> http://pubs.acs.org/doi/full/10.1021/ct4010307]
>
> Dynamics is another matter. Langevin thermostats removes momentum transfer
> and changes the rate dynamics, despite it samples the canonical ensemble
> ... if the system is ergodic in practice. Two different simulations can
> converge, if the string of random numbers used in langevin thermostats is
> the same. I'm not sure about V-rescaling.
>
> I agree that all thermostats and barostats likely cause some artifacts in
> dynamics.
>
>
> On Sat, Oct 11, 2014 at 5:29 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
> wrote:
>
>> Well, if it does not conserve total energy, than such a computational
>> experiment is not reliable. This is a sad truth.
>>
>> Philosophically, you have two options here. Either you accept that
>> energy leakage is significant and then you must fight against it
>> (smaller time-step, double precision, constraints, etc), or -- on the
>> contrary -- you say that energy loss can be neglected and proceed "as
>> is".
>>
>> My personal rule is if the system does not lose more than 2% of total
>> energy during an entire run, the result is acceptable. I can be
>> criticized for this voluntary assumption, obviously.
>>
>> Anyway, tricks with T-coupling constitute a very bad idea in this
>> case. You basically try to mask the energy leakage problem with the
>> thermostat. Thermostat never removes the problem itself.
>>
>>
>> Dr. Vitaly V. Chaban
>>
>> Виталий Витальевич ЧАБАН
>>
>>
>> On Sat, Oct 11, 2014 at 11:12 PM, Johnny Lu <johnny.lu128 at gmail.com>
>> wrote:
>> > I tried NVE on single precision gromacs 4.6.7 with and without GPU.
>> > The energy either drift down or up, depending on the mdp file, and the
>> drift
>> > seems linear.
>> >
>> > Linear fit says that if I run 100 ns simulation, at the end the energy is
>> > doubled.
>> >
>> > If I use double precision gromacs, the drift seems insignificant over
>> 100 ns
>> > simulation by linear regression fitting on a 300 ps run.
>> > But double precision gromacs can't use gpu and is much slower than single
>> > precision gromacs.
>> >
>> > On Sat, Oct 11, 2014 at 4:33 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
>> > wrote:
>> >>
>> >> I also cannot get why not to just turn off the thermostat...
>> >>
>> >> If energy transfer phenomena are in focus, NVE is an ensemble of
>> >> choice, no matter which relaxation constant is used for the T-coupling
>> >> algorithm.
>> >>
>> >>
>> >> Dr. Vitaly V. Chaban
>> >>
>> >> Виталий Витальевич ЧАБАН
>> >>
>> >>
>> >> On Sat, Oct 11, 2014 at 6:32 PM, Antonio Baptista <baptista at itqb.unl.pt
>> >
>> >> wrote:
>> >> > Then, run true NVE, for the reasons we already pointed.
>> >> >
>> >> > On Sat, 11 Oct 2014, Johnny Lu wrote:
>> >> >
>> >> >> For dynamics with correct rate and correct fluctuation.
>> >> >>
>> >> >> On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban <
>> vvchaban at gmail.com>
>> >> >> wrote:
>> >> >>
>> >> >>> what is it needed for?
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> Dr. Vitaly V. Chaban
>> >> >>>
>> >> >>> Виталий Витальевич ЧАБАН
>> >> >>>
>> >> >>>
>> >> >>> On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu <johnny.lu128 at gmail.com>
>> >> >>> wrote:
>> >> >>> > Hi.
>> >> >>> >
>> >> >>> > Is it a good idea to mimic NVE by a NVT simulation with a large
>> >> >>> temperature
>> >> >>> > coupling time constant, to reduce the effect of the thermostat ?
>> >> >>> >
>> >> >>> > If I use V-rescale thermostat, what artifacts will the simulation
>> >> >>> > get
>> >> >>> > if
>> >> >>> I
>> >> >>> > use a large coupling time (say, 500 ps) and single precision
>> gromacs
>> >> >>> > ?
>> >> >>> >
>> >> >>> > Thank you.
>> >> >>> > --
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