[gmx-users] MD after equilibration phase

[bipin singh]

When we mention
gen_vel=no ;And provide pdb as input with no velocities

As mentioned in the manual:
"The velocities are set to zero when there are no velocities in the input
structure file"

Please elaborate what does this sentence mean.

On Fri, Apr 6, 2012 at 19:10, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> bipin singh wrote:
>
>> Also, if we give continuation=yes in mdp file and use input as pdb file
>> as input instead of gro file, grompp never complains....I don't no how it
>> reads velocities from pdb file (as no velocities are present in pdb files).
>> Ideally it should complain that no velocities found in input file....
>>
>>
> Again, the "continuation" keyword has nothing to do with velocities.  If
> you have "gen_vel = no" and you provide a .pdb file with no velocities,
> then you do not preserve velocity information.  Whatever the initial forces
> are govern the resulting motions.  In any case, you do not preserve the
> previous simulation conditions.
>
> -Justin
>
>  On Fri, Apr 6, 2012 at 12:42, Peter C. Lai <pcl at uab.edu <mailto:
>> pcl at uab.edu>> wrote:
>>
>>    On 2012-04-06 11:05:51AM +0400, James Starlight wrote:
>>     > Dear Gromacs users!
>>     >
>>     >
>>     > I have small question about order of the runs and input data.
>>     >
>>     > Ussually I do 2 equilibration phases and subsequent productive
>>    phase in the
>>     > conditions wich are equal to the last equilibration phase ( e.g
>>    often this
>>     > is npt ).
>>     >
>>     > In the second equil.mdp and md.mdp there is option
>>     >
>>     > continuation             = yes
>>     >
>>     > which means that there have been previous phases of the
>>    simulation from
>>     > wich  coordinates and velocities should be taken.
>>     >
>>     > As I understood the coordinates is taken from .gro file but from
>>    what file
>>     > the velocities must be providen ? Does it .cpt checkpoint file from
>>     > previous run? In some cases I've forgotten to define -t npt.cpt
>>    for my MD
>>     > run providing only coordinates in GRO file, topology and md.mdp
>>    but I have
>>     > not seen any errors in such simulation due to absence of that
>>    .cpt and
>>     > GROMPP never remind me of the absense of this file. What exactly
>>    is in that
>>     > .cpt file and from wich source the velocities from equilibration
>>    phase are
>>     > taken ?
>>
>>    continuation = yes is telling LINCS that it is a continuation and
>>    it should not attempt to refit the constrained bonds on the first pass.
>>
>>    The coords, velocities, state, and box information are taken either
>>    from the
>>    cpt file or you can specify the previous .trr and it will take the
>>    last frame
>>    from that and use it. If you used the output gro file without -t, then
>>    it will take coordinates and velocities from the .gro but the
>>    problem there
>>    is the limited precision (3 decimal points for each).
>>
>>    --
>>    ==============================**==============================**======
>>    Peter C. Lai                    | University of Alabama-Birmingham
>>    Programmer/Analyst              | KAUL 752A
>>    Genetics, Div. of Research      | 705 South 20th Street
>>    pcl at uab.edu <mailto:pcl at uab.edu>                     | Birmingham AL
>>
>>    35294-4461
>>    (205) 690-0808                  |
>>    ==============================**==============================**======
>>
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>>
>>
>> --
>> -----------------------
>> /Regards,/
>> Bipin Singh
>>
>>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
>
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-- 
-----------------------
*Regards,*
Bipin Singh
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