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

[Justin A. Lemkul]

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

-- 
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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

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