# [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
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
>correct.
>

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

-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

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