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

Sanku M msanku65 at yahoo.com
Wed Aug 3 03:38:20 CEST 2011

Hi Justin,
  So, do you suggest that after minimization, I should generate the velocity at 
300K instead ?
i.,e for equilibration,should following the set-up?

gen-vel                  = yes
>>  gen-temp                = 300
>>  gen-seed                = -1

From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tue, August 2, 2011 8:26:16 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

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 

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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