[gmx-users] NVT-Eq ---> NVT-MD

[Alexander Alexander]

Great explanation, thanks.
I hope you mean with "atoms have velocities" the last three columns in .gro
file you mean.

So, If I recall my first question concerning to the combining of two
sequence NVT-Eq and NVT-MD to just one longer NVT-MD after minimization
directly, then I need to turn on the velocity generation in my single
NVT-MD production.

Regards,
Alex


On Mon, Feb 15, 2016 at 6:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/15/16 12:40 PM, Alexander Alexander wrote:
>
>> Dear Mark,
>>
>> To be honest, I do not know exactly when and in which physics the velocity
>> generation in a MD simulation is necessary and when not !
>>
>> And I usually-historically generate velocity in the Equilibration and not
>> in Production.
>>
>> My specific case here is a pure metallic surface.
>>
>>
> Here is a simple decision structure:
>
> Do the atoms have velocities?
> If yes, don't re-generate them.
> If no, you need to generate them.
>
> gen_vel randomly assigns velocities according to a Maxwell distribution.
> If you're continuing a previous run, you already have velocities that are
> (presumably) part of the target statistical mechanical ensemble.
> Re-generating them destroys that and requires re-equilibration.  If you're
> just starting out, you've probably done an energy minimization, which has
> no velocities.  So if you try to start a simulation without generating
> velocities, your system may behave rather strangely as the thermostat tries
> to figure out how to bring the non-existent velocities into agreement with
> the target temperature.
>
> -Justin
>
>
> Regards,
>> Alex
>>
>> On Mon, Feb 15, 2016 at 6:27 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>> Hi,
>>>
>>> Why did your two-part run need to generate velocities at a suitable
>>> temperature in the first part? Does that reason apply to your one-part
>>> run?
>>> ;-)
>>>
>>> Mark
>>>
>>> On Mon, Feb 15, 2016 at 6:23 PM Alexander Alexander <
>>> alexanderwien2k at gmail.com> wrote:
>>>
>>> Thanks for your prompt response,
>>>>
>>>> Could you please confirm me that  in my single NVT-MD I should  use
>>>> "continuation  = no" and below velocity generation, right? or velocity
>>>> generation is not required any more?
>>>>
>>>> ;Generate velocity
>>>> gen_vel = yes
>>>> gen_temp = 298.15
>>>> gen_seed = -1
>>>>
>>>> Regards,
>>>> Alex
>>>>
>>>> On Mon, Feb 15, 2016 at 6:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>>
>>>>> On 2/15/16 12:09 PM, Alexander Alexander wrote:
>>>>>
>>>>> Dear Gromacs user,
>>>>>>
>>>>>> I have an elementary question which I would be thankful if one could
>>>>>> comment on it;
>>>>>>
>>>>>> I want to do a NVT-MD simulation as a production calculation of my MD
>>>>>> simulation for 10 ns, and suppose that a NVT- Equilibration has been
>>>>>>
>>>>> done
>>>>
>>>>> in advance for 0.5 ns. The normal differences between their .mdp files
>>>>>>
>>>>> are
>>>>
>>>>> coming below and the rest of their .mdp files are fully identical;
>>>>>>
>>>>>> NVT-Eq (Equilibration)
>>>>>> ------------------------------------
>>>>>> nsteps  =  500000    ; 0.5 ns
>>>>>>
>>>>>> ;Generate velocity
>>>>>> gen_vel = yes
>>>>>> gen_temp = 298.15
>>>>>> gen_seed = -1
>>>>>> -------------------------------------
>>>>>>
>>>>>>
>>>>>> NVT-MD (Production)
>>>>>> -------------------------------------
>>>>>> nsteps = 10000000    ; 10 ns
>>>>>> continuation  = yes    ;continuing from NVT-Eq
>>>>>>
>>>>>>
>>>>>> ;Generate velocity
>>>>>> gen_vel = no
>>>>>> -------------------------------------
>>>>>>
>>>>>> Since they have identical .mdp parameters, then, my question is that:
>>>>>>
>>>>>> if it is possible to do just one NVT-MD simulation (a bit longer (10 +
>>>>>> 0.5)ns ) instead of two sequence NVT-Eq and NVT-MD simulations?
>>>>>>
>>>>>>
>>>>>> Of course.  The normal use for separating two phases (equilibration
>>>>> and
>>>>> production) is in the case of restraints, shorter time step for
>>>>> equilibration in troublesome systems, etc.  If you just have the same
>>>>> settings, do a single run.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>
>>>>> ==================================================
>>>>> --
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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