[gmx-users] Continuation = yes keyword

[Justin Lemkul]

On 8/5/19 10:08 PM, Bratin Kumar Das wrote:
> Hi,
> In MD simulation the initial velocity is generated by the Maxwell
> distribution..Therefore in nvt equilibration we generate the velocity by
> keeping gen-vel= yes. In the next equilibration step or production md step
> the generated velocity is read by .cpt file. Therefore if we do
> continuation = no ...along with gen-vel=no ...It may give error
> message...Otherwise if we use continuation=no...Along with gen-vel=yes...It
> will produce new velocity...Which won't be a continuous simulation..

Beyond compatibility of keywords, the "continuation" setting affects 
constraints. If you say "no," then mdrun will constrain the 
configuration it is supplied, assuming that no constraints have yet been 
solved since it is a new run. If the coordinates supplied are from a 
previous simulation with constraints, then you are likely going to 
change them slightly, thus introducing a discontinuity.

-Justin

> On Tue 6 Aug, 2019, 4:01 AM Dawid das, <addiw7 at googlemail.com> wrote:
>
>> Dear All,
>>
>> I start my MD simulation from a previous run using data in tpr and cpt
>> files
>> with changed mdp options for the new simulation.
>> Is it really important to use "continuation = yes" for the lincs
>> constraints.
>> What can be wrong if I don't (I use continuation = no).
>>
>> Best wishes,
>> Dawid Grabarek
>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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