[gmx-users] Continuation=yes From?
mohsen ramezanpour
ramezanpour.mohsen at gmail.com
Mon May 2 14:27:35 CEST 2011
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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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