[gmx-users] Heating step by step.

[Justin Lemkul]

On 9/5/15 9:30 AM, Dawid das wrote:
> 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
>
> ?
>

Of course.  I was only correcting the SA settings.  If you're heating from 0 to 
300 K, though, don't generate velocities at 20 K.

-Justin

> 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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-- 
==================================================

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

==================================================