[gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Justin,


1) I've defined 5 steps for specified definition of the time of each step
as well as for more flexibile controle of the such annealing: e.g I want
that equilibration step corresponded to the temperature between 320 and
330K will be longer than between first step corresponded to 300-310K etc


2) About velosities. As I understood for annealing equilibration gen_temp
must be equal to the starting temperature of such equilibration ( gen_temp=
300 in the above example). But in what exactly circumstances the changing
in gen_temp could be usefull? As I've told after such annealing
equilibration I want to simulate my system on the high temperature
condition for efficient conformation sampling. Might it be that initial
high velocities could be usefull for such sampling efficacy?

James


4 апреля 2012 г. 17:25 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:

>
>
> James Starlight wrote:
>
>> Justin,thanks!
>>
>>
>> 1) For example for the situation presented in manual for 2 groups with 3
>> and 4 points the time enty should be
>>
>> annealing_time = 0 3 6 0 2 4 6
>>
>> from this I've understood that 0 value is the start of timer for each
>> group and subsequent values are the actual time in the ps, havennt it ?
>>
>>
> Yes.
>
>
>  For example I'd like to perform nvt simulation ( with overal time 100ps)
>> for three different groups in 5 equal steps. So does annealing options must
>> be
>> annealing = single single single
>> annealing_npoints = 5 5 5
>> annealing_time = 0 25 50 75 100 0 25 50 75 100 0 25 50 75 100
>>
>> annealing_temp = 300 310 320 330 340 350 300 310 320 330 340 350 300 310
>> 320 330 340 350
>> # this means that for each group temperature increase on 10K on each step
>> and there are 5 steps for each grou ( equal to npoints)
>>
>>
> I don't understand why 5 steps are necessary.  You're doing a linear
> increase from 300K to 350K for all groups over 100 ps.  All you need is:
>
>
> annealing = single single single
> annealing_npoints = 2 2 2
> annealing time = 300 350 300 350 300 350
>
>  Does this ecxample correct or there are some connection between that
>> values for diffent groups ?
>>
>> 2) How I can couple this annealing options with the *gen_temp* values
>> wich as I understood must also differs on the each step ? OR should I use
>> some averaged gen_temp?
>>
>>
> The value of gen_temp is only used for initial velocity generation, so in
> your case it should still be set to 300.  After that, it is irrelevant.  Do
> you mean ref_t?  In this case, the annealing temperature values override
> ref_t, so it doesn't matter.
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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