[gmx-users] Re: gen_temp, gen_seed

[Justin A. Lemkul]

Steven Neumann wrote:
> Dear Gmx Users, Dear Justin
>  
> I am wondering which approach for generating velocities in protein or 
> protein-ligand system is a proper one:
>  
> a) 
> NVT   gen_vel = yes
>           gen_temp=298
>           gen_seed=-1
> NPT   gen_vel=no
> MD    gen_vel=no
>  
> b)
> NVT   gen_vel = yes
>           gen_temp=298
>           gen_seed=-1
> NPT   gen_vel=no
> MD    gen_vel = yes
>           gen_temp=298
>           gen_seed=-1
>  
> As I always used the approach a) I saw in Justin's tutorial (Protein and 
> ligand) b). However, in protein in water tutorial he used the approach 
> a). I am confused, can you please help?
>  

There was a typo in the tutorial.  Approach (a) is correct.  After 
equilibration, regenerating velocities destroys the equilibrated ensemble.

I have fixed the tutorial's .mdp file.  Thanks for pointing out the mistake.

-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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