[gmx-users] Continuation=yes From?

[mohsen ramezanpour]

Thank you for your detailed axplain
I understood completely

On Mon, May 2, 2011 at 4:34 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> Thank you for your reply
>> My  is Protein-ligand,It is have the same conditions as tutorial.I did
>> pull ligand in the z direction.
>> Actualy I found your note about gen_vel ,but I didn't any  about
>> Continuation!
>>
>>
> Not that specific keyword, no, but I do address the general principle about
> continuing these simulations via this very discussion about gen_vel.
>
>
>  You are right,But there is another problem:
>> You have not used any    -t     option   in grompp command (doing umbrella
>> step).
>>
>>
> Correct.  See the discussion on gen_vel that I referenced earlier.
>
>
>  Since we have set Continuation=yes;
>> Can grompp realize from which .cpt (npt.cpt  )  it must  use ?
>>
>>
> grompp does not make any choice about what it should use.  It takes
> whatever input you give it and assembles a run input file.  If you're
> following my procedure (which may or may not necessarily be applicable in
> all cases), then there will NOT be a suitable .cpt file for each starting
> configuration.  These configurations were generated using SMD, and .cpt
> files are not written and saved at every frame so you have a corresponding
> one later.
>
>
>  And my last question:
>> Do I need to any .cpt file ? (Because I have set Continuation=yes)
>>
>>
> Checkpointing and continuation are related, but not identical.  The
> "continuation" keyword deals with whether or not constraints are solved
> before the first integration step.  It otherwise has nothing to do with the
> thermodynamic state of the system, which is contained in the .cpt file.
>
> For your system, as I state in the tutorial, you may want to set "gen_vel =
> yes" in each window (since there is no prior equilibration, which may be a
> problem for some systems, but not the tutorial example).  This would
> eliminate the need for a .cpt file.
>
> -Justin
>
>  Thanks in advance
>>
>>
>>
>>
>>
>> On Mon, May 2, 2011 at 3:27 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    mohsen ramezanpour wrote:
>>
>>        Dear Dr.Justin
>>
>>        Regarding Umbrella Sampling tutorial:
>>
>>        The CONTINUATION option in md_umbrella.mdp is YES,
>>        and you have noticed : From NPT
>>
>>        I can't understand it's reason correctly!
>>
>>
>>    This is a meaningless comment.  It was left there from copying and
>>    pasting files before modifying them.  The important part is that
>>    "continuation = yes" be set to correctly solve the constraints.
>>
>>
>>        we run a NPT and then Pulling, then extracted some
>>        configurations from pull.trr file.
>>        I think we must continue from pull.cpt    not   NPT.cpt
>>
>>        I mean :
>>        grompp   -f  md_umbrella.mdp .............................  -t
>>      pull.cpt  is more correct than
>>
>>        grompp    -f md_umbrella.mdp .............................. -t
>>         NPT.cpt
>>
>>        am I right?
>>
>>
>>    In the case of the tutorial, no.  There is not a corresponding .cpt
>>    file for each configuration generated.  If you were to somehow apply
>>    the same .cpt file for each configuration, almost certainly some of
>>    the windows would blow up because the initial velocities would cause
>>    nasty collisions.  Note that I discuss the continuation issue,
>>    proper settings for gen_vel, etc. in the tutorial, step six.
>>
>>    -Justin
>>
>>
>>        Thanks in advance for your reply
>>
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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>>
> --
> ========================================
>
> 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
>
> ========================================
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