[gmx-users] Velocity generation

[Justin A. Lemkul]

Juliette N. wrote:
> Dear gmx users,
>  
> I have two short questions about generation of initial velocities in 
> simulations. If I want to run simulations at for example 400 K do I have 
> to alter the temperature for maxwell distribution settings? ( I mean 
> gen_temp            =  400? )        
> 

Yes, otherwise the initial velocity distribution is wrong and your thermostat 
will have to make some large compensations to reach the target temperature.

> gen_vel             =  yes                 
> gen_temp            =  300.0         > 400 ?      
> gen_seed            =  173529       
> 
> - Also If I want to do simulated annealing for the target T= 400 K, 
> should I anneal to higher T than 400, say 500K and cool down to 400 or 
> SA is only applicable at lower target temperatures like 300K ?
>  

You can do whatever you like.  People sometimes even use SA up to 1000 K or more.

-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

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