[gmx-users] High Initial generated Temp

[Justin Lemkul]

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://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

========================================