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

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 3 03:26:16 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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