[gmx-users] High Initial generated Temp

[tarak karmakar]

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?

Thanks,
Tarak


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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