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 <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@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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