[gmx-users] High Initial generated Temp
Mark Abraham
mark.j.abraham at gmail.com
Wed Jun 5 15:41:36 CEST 2013
On Wed, Jun 5, 2013 at 3:06 PM, tarak karmakar <tarak20489 at gmail.com> wrote:
> One more query Justin.
> Even if I don't use any sort of constraints in the final run, I'm not
> getting the initial temperature as exactly 300 K. Initial part of the .log
> file is as follows
>
>
> Initial temperature: 297.694 K
>
> Started mdrun on node 0 Wed Jun 5 16:58:40 2013
>
> Step Time Lambda
> 0 0.00000 0.00000
>
> Energies (kJ/mol)
> Bond U-B Proper Dih. Improper Dih. CMAP Dih.
> 8.53037e+03 1.41675e+04 8.92031e+03 8.51469e+02 -2.03250e+03
> LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
> 4.38857e+03 7.54455e+04 3.60795e+05 -8.59592e+03 -2.71243e+06
> Coul. recip. Potential Kinetic En. Total Energy Temperature
> -2.16435e+05 -2.46639e+06 4.69142e+05 -1.99725e+06 2.97697e+02
> Pres. DC (bar) Pressure (bar)
> 0.00000e+00 2.49064e+02
>
>
> Is it the normal case in gromacs? Or, it is because of my system?
> I see in lammps, generating the initial temp shows the exact number as
> specified in the input file at zeroth step. (not my system but a small test
> system)
>
GROMACS is doing what was asked of it - see manual 7.3.17. The distribution
of values sampled from a given distribution generally will not have an
average that equals that given distribution. Whatever LAMMPS does is its
own business :-)
Mark
On Wed, Jun 5, 2013 at 1:57 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 6/4/13 12:51 PM, tarak karmakar wrote:
> >
> >> Yeah!
> >> It is indeed a silly point to generate a velocity distribution at 0 K. (
> >> Maxwell-Boltzmann will be in trouble)
> >> After the warm up, now let say my protein is in 300 K, can't I generate
> a
> >> velocity distribution at 300 k (using the keyword gen_vel = yes,
> gen_temp
> >> =
> >> 300 K gen_seed = 173529 ) during my production run?
> >>
> >>
> > You can generate velocities whenever you like, but you'll have to allow
> > for some time to equilibrate, so what you're calling "production" isn't
> > entirely production because it's no longer equilibrated in any real
> sense.
> > The heating phase may help to optimize the initial geometry, but
> > regenerating velocities may screw everything up if something becomes
> > unstable. Assuming restraints are off during "production," then you can
> > screw up the geometry of your system if something gets an unpleasant kick
> > from the new velocities.
> >
> > -Justin
> >
> > On Tue, Jun 4, 2013 at 10:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >>
> >>>
> >>> On 6/4/13 12:17 PM, tarak karmakar wrote:
> >>>
> >>> Thanks Justin.
> >>>> Sorry for not uploading the full .mdp. Here it is,
> >>>>
> >>>> ; 7.3.3 Run Control
> >>>> integrator = md
> >>>> tinit = 0
> >>>> dt = 0.001
> >>>> nsteps = 5000000
> >>>> nstcomm = 1
> >>>> comm_grps = system
> >>>> comm_mode = linear
> >>>> energygrps = system
> >>>>
> >>>> ; 7.3.8 Output Control
> >>>> nstxout = 5000
> >>>> nstfout = 5000
> >>>> nstlog = 1000
> >>>> nstenergy = 1000
> >>>> nstxtcout = 1000
> >>>> xtc_precision = 1000
> >>>> xtc_grps = System
> >>>>
> >>>> ; 7.3.9 Neighbor Searching
> >>>> nstlist = 10
> >>>> ns_type = grid
> >>>> pbc = xyz
> >>>> rlist = 1.2
> >>>> rlistlong = 1.4
> >>>>
> >>>> ; 7.3.10 Electrostatics
> >>>> coulombtype = PME
> >>>> rcoulomb = 1.2
> >>>> fourierspacing = 0.12
> >>>> pme_order = 4
> >>>> ewald_rtol = 1e-5
> >>>>
> >>>> ; 7.3.11 VdW
> >>>> vdwtype = switch
> >>>> rvdw = 1.2
> >>>> rvdw-switch = 1.0
> >>>>
> >>>> DispCorr = Ener
> >>>>
> >>>>
> >>>> ; 7.3.14 Temperature Coupling
> >>>> tcoupl = nose-hoover
> >>>> tc_grps = system
> >>>> tau_t = 1.0
> >>>> ref_t = 300
> >>>>
> >>>> ; 7.3.15 Pressure Coupling
> >>>> pcoupl = parrinello-rahman
> >>>> pcoupltype = isotropic
> >>>> tau_p = 1.0
> >>>> compressibility = 4.5e-5
> >>>> ref_p = 1.0
> >>>>
> >>>> gen_vel = yes
> >>>> gen_temp = 300
> >>>> gen_seed = 93873959697
> >>>>
> >>>> ; 7.3.18 Bonds
> >>>> constraints = h-bonds
> >>>> constraint_algorithm = LINCS
> >>>> continuation = yes
> >>>> lincs_order = 4
> >>>> lincs_iter = 1
> >>>> lincs_warnangle = 30
> >>>>
> >>>> Note: Using CHARMM27 force field
> >>>>
> >>>> I didn't use the 'continuation' part here.
> >>>> In the heating run I didn't put any constraints but in the production
> >>>> MD,
> >>>> I
> >>>> do apply constraints to the covalent bonds involving hydrogens. I just
> >>>> want
> >>>>
> >>>>
> >>> The introduction of constraints explains the observed behavior. You
> ran
> >>> an unconstrained simulation, then at step 0 of the constrained
> >>> simulation,
> >>> the constraints have to be satisfied, which may introduce sudden
> movement
> >>> in atomic positions, hence large velocities and a high temperature.
> The
> >>> rule of thumb I always use - if you're going to use constraints during
> >>> production simulations, use constraints during equilibration. I have
> >>> seen
> >>> several instances where unconstrained equilibration causes constrained
> >>> simulations to later fail.
> >>>
> >>>
> >>> to test the ligand movement inside the protein cavity in different
> set
> >>> of
> >>>
> >>>> initial velocities to get the feelings of how ligand is interacting
> with
> >>>> certain residues.
> >>>> So, then should I use these different velocity generating seeds during
> >>>> the
> >>>> warm up step?
> >>>>
> >>>>
> >>>> That's an interesting question. If you're warming from 0 -> 300 K, I
> >>> don't know how grompp will generate velocities at 0 K, but regenerating
> >>> velocities after warming seems to defeat the purpose of doing the
> warming
> >>> at all, in my mind, since you're just going to re-randomize the entire
> >>> system by doing so.
> >>>
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==============================****==========
> >>>
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Research Scientist
> >>> Department of Biochemistry
> >>> Virginia Tech
> >>> Blacksburg, VA
> >>> jalemkul[at]vt.edu | (540) 231-9080
> >>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<
> http://vt.edu/Pages/Personal/justin>
> >>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>> >
> >>>
> >>> ==============================****==========
> >>>
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> > --
> > ==============================**==========
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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