[gmx-users] Heating step by step.

[Dawid das]

Yes, that is right Justin. But I still need:
tcoupl          = V-rescale                 ; modified Berendsen thermostat
tc-grps         = Protein non-Protein   ; two coupling groups - more
accurate
tau_t           = 0.1     0.1           ; time constant, in ps
ref_t           = 300     300           ; reference temperature, one for
each group,

lines as well as those:

; Velocity generation
gen_vel         = yes           ; assign velocities from Maxwell
distribution
gen_temp        = 20            ; temperature for Maxwell distribution

?

Best regards,
Dawid

2015-09-05 13:30 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 9/5/15 5:48 AM, Dawid das wrote:
>
>> I struggle to properly define my *mdp file. I have following keywords and
>> their values:
>>
>> ;Simulated annealing is on
>> annealing           = single
>> annealing-npoints   = 30 30
>> annealing-time      = 0.0 0.002 5.0 5.002 10.0 10.002 15.0 15.002 20.0
>> 20.002 25.0 25.002 30.0 30.002 35.0 35.002 40.0 40.002 45.0 45.002 50.0
>> 50.002 55.0 55.002 60.0 60.002 65.0 65.002  75.0 75.002 0.0 0.002 5.0
>> 5.002
>> 10.0 10.002 15.0 15.002 20.0 20.002 25.0 25.002 30.0 30.002 35.0 35.002
>> 40.0 40.002 45.0 45.002 50.0 50.002 55.0 55.002 60.0 60.002 65.0 65.002
>> 75.0 75.002
>> annealing-temp      = 0 20 20 40 40 60 60 80 80 100 100 120 120 140 140
>> 160
>> 160 180 180 200 200 220 220 240 240 260 260 280 280 300 0 20 20 40 40 60
>> 60
>> 80 80 100 100 120 120 140 140 160 160 180 180 200 200 220 220 240 240 260
>> 260 280 280 300
>>
>>
>> ; Temperature coupling is on with annealing
>> tcoupl          = V-rescale                 ; modified Berendsen
>> thermostat
>> tc-grps         = Protein non-Protein   ; two coupling groups - more
>> accurate
>> tau_t           = 0.1     0.1           ; time constant, in ps
>> ref_t           = 300     300           ; reference temperature, one for
>> each group, in K
>>
>> so I want to anneal two groups as you may see. However, grompp says:
>>
>> Fatal error:
>> Not enough annealing values: 1 (for 2 groups)
>>
>> I believe I do everything according to the documentation.
>>
>>
> Then you need:
>
> annealing = single single
>
> Also note that your approach is needlessly complicated.  You want a simple
> linear increase, yes?  That's straightforward:
>
> annealing-npoints = 2 2
> annealing-time = 0  75  0  75
> annealing-temp = 0  300 0  300
>
> -Justin
>
> 2015-09-04 22:41 GMT+01:00 Dawid das <addiw7 at googlemail.com>:
>>
>>
>>> 2015-09-04 22:03 GMT+01:00 Vitaly V. Chaban <vvchaban at gmail.com>:
>>>
>>> However, your simulation schedule makes little sense physically .
>>>>
>>>>
>>>
>>> What do you mean by that? I just want to heat up my system gently before
>>> equilibration phase.
>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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