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

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 3 03:40:21 CEST 2011

```
Sanku M wrote:
> 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?
>

You should always equilibrate under the desired conditions.  Never make sudden
changes, or else you're going to damage the stability of the system.

-Justin

> 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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--
========================================

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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