From: Zhao Lina (lordlnzhao_at_gmail.com)
Date: Wed Dec 17 2014 - 19:31:49 CST
Hi Jeff,
Thanks a lot for your clear explanation!
Do you think the difference is insignificant after molecular dynamics
up to several tens of nanoseconds?
Best regards,
Lina
2014-12-17 19:45 GMT+08:00, Jeff Comer <jeffcomer_at_gmail.com>:
> The difference is that without reinitvels you are starting with a
> temperature of zero. If you have a thermostat (langevin on, for
> instance) it should pull the temperature up to desired after a few
> thousand or so steps (depending on langevinDamping); however, it's
> better to begin with a reasonable temperature.
>
> Jeff
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
>
>
> On Wed, Dec 17, 2014 at 3:03 AM, Zhao Lina <lordlnzhao_at_gmail.com> wrote:
>> Dear all,
>>
>> In *.conf file, there are 2 commands for minimization as minimize and
>> reinitvels. Then it can perform an equilibrium run. The commands looks
>> like:
>> minimize 1000 ；
>> reinitvels $temperature ；
>> run 50000 ; # 100ps
>>
>> But I found when reinitvels was commented or deleted as:
>> minimize 1000 ；
>> run 50000 ; # 100ps
>> The equilibrium running still could be performed smoothly. Although,
>> there is no reinitvels to redistribute the velocities for atoms, the
>> velocities of the molecules and atoms in equilibrium run are not zero
>> obviously. These atoms seems act with the normal random velocities
>> according to the temperature set of *.conf file.
>>
>> So I'm wondering whether reinitvels is necessary before an equilibrium
>> run? What's the real difference between setting reinitvels or not?
>> Thanks a lot for your ideas!
>>
>> Lina
>>
>
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