[gmx-users] Re: Simulation in the high temperature conditions
jmsstarlight at gmail.com
Wed Apr 4 16:10:12 CEST 2012
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?
4 апреля 2012 г. 17:25 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:
> James Starlight wrote:
>> 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 ?
> 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
>> 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 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
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