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

[Alexander Alexander]

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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