[gmx-users] High Initial generated Temp

[tarak karmakar]

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
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?

Thanks,
Tarak







On Tue, Jun 4, 2013 at 5:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/4/13 8:07 AM, tarak karmakar wrote:
>
>> Dear All,
>>
>> Although I have set gen_temp = 300, it is showing the initial temperature
>> 445.7 K, generated at the very beginning  of the run.
>>
>> gen_vel                 = yes             ; velocity generation
>> gen_temp                = 300
>> gen_seed                = 93873959697
>>
>> Is it because of a bad geometry? In mailing list I came across this thread
>> [ http://comments.gmane.org/**gmane.science.biology.gromacs.**user/41931<http://comments.gmane.org/gmane.science.biology.gromacs.user/41931>
>> ]
>> Prior to this production run, I heated my system slowly from 0 K to 300 K
>> within 300 ps time span.
>> It would be very helpful if someone suggests me the way to deal with this
>> problem?
>>
>>
> A full .mdp file is always more useful than a small snippet.  I have seen
> this same behavior when the "continuation" parameter is incorrectly set -
> have you used "continuation = yes" in your .mdp file?  If not, the
> constraints get messed up and your initial velocities can get all messed up.
>
> A larger point is this - why are you re-generating velocities after
> heating the system from 0 to 300 K?  Why not simply preserve the ensemble
> at 300 K by using a .cpt file?
>
> -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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