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

[Justin Lemkul]

On 2/15/16 12:22 PM, Alexander Alexander 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?
>

Velocities should be generated at the beginning of a run (gen_vel = yes), and 
preserved (gen_vel = no) if the run is continued after being stopped.

The same applies with the "continuation" keyword.  Is it the start of a brand 
new run?  Continuation = no.  Is it a continuation of a previous run that was 
stopped?  Continuation = yes.

-Justin

> ;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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

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

==================================================