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)
On Wed, Jun 5, 2013 at 1:57 AM, Justin Lemkul <jalem...@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 <jalem...@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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