[gmx-users] Problem with temperature and stochastic dynamics in FEP

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> Sanku M wrote:
>> Hi Justin,
>>   I first performed two minimization using steep and l-bfgs as the 
>> method on the solvated system for each lambda. Then I ran a 500ps NVT 
>> simulation on minimized system ( for each lambda) where essentially 
>> same .mdp file was used except the following change:
>>    gen-vel                  = yes
>>  gen-temp                = 280
>>  gen-seed                = -1
>>
>> So, essentially, I heated the minimized system up from 280 K with 
>> ref_t 300K using sd integrator. But, here also I found the average 
>> temperature goes to 303 K( instead of 300 K) .
> 
> Unless you did simulated annealing in between, you didn't heat the 
> system, you suddenly jolted the temperature, which is probably not 
> stable.  Maybe the integrator/Langevin thermostat does not react well to 
> these conditions. Equilibrate under the conditions you wish to collect 
> data.  Your data collection uses NPT, so running NVT at a different 
> temperature and suddenly changing the temperature and introducing 
> pressure coupling is not an appropriate procedure. If nothing else, your 
> data will be unreliable, even if your temperature was correct.
> 

Sorry, misread the previous .mdp settings.  You're still using NVT, but the 
point about the temperature is still valid here.

-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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