[gmx-users] Heating step by step.

[Dawid das]

O'right, it seems that I did everything correctly.
Thank you for your help! :)

2015-09-05 14:30 GMT+01:00 Dawid das <addiw7 at googlemail.com>:

> 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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>
>