[gmx-users] Continuation=yes From?

[Justin A. Lemkul]

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

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