[gmx-users] High Initial generated Temp

[Justin Lemkul]

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

-- 
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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

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