[gmx-users] High temperature Simulation

[Kavyashree M]

Hello,

The set pressure should reflect whatever system you are trying to model.
>

This statement is not very clear to me.. But when the mdout.mdp file after
grompp
during energy minimization is examined it says -

gen-vel                  = no
gen-temp                 = 300
gen-seed                 = 173529

Even though I have not assigned any velocities in em.mdp file. Thats the
reason why got this doubt about temperature during energy minimization.

Thank you
With Regards
Kavya


>
> -Justin
>
>  Thank you
>> With Regards
>> Kavya
>>
>> On Mon, Oct 17, 2011 at 3:29 PM, bipin singh <bipinelmat at gmail.com<mailto:
>> bipinelmat at gmail.com>> wrote:
>>
>>    As far as I know we do energy minimization at room temperature only.
>>    Only during equilibration
>>    (NVT and NPT) we use high temperature for maintaining proper density
>>    before starting the final production run.
>>
>>    On Mon, Oct 17, 2011 at 15:15, Kavyashree M <hmkvsri at gmail.com
>>    <mailto:hmkvsri at gmail.com>> wrote:
>>     > Dear users,
>>     >
>>     > For simulating a protein at high temperature (more than 300K,
>>     > less than 400K) using OPLSAA forcefield, what are the parameters
>>     > other than Temperature that need to be taken care of?
>>     > Does the energy minimization step also needs to be done at high
>>     > temperature? (here my aim is not to simulate an unfolding event)
>>     > I have a reference -
>>     > Biophysical Journal Volume 94 June 2008 4444–4453
>>     >
>>     > Any other references or suggestions will be helpful.
>>     >
>>     > Thanking you
>>     > With Regards
>>     > M. Kavyashree
>>     >
>>     >
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>>    --
>>    -----------------------
>>    Regards,
>>    Bipin Singh
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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