[gmx-users] Continuation=yes From?

[mohsen ramezanpour]

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!

You are right,But there is another problem:
You have not used any    -t     option   in grompp command (doing umbrella
step).

Since we have set Continuation=yes;
Can grompp realize from which .cpt (npt.cpt  )  it must  use ?

And my last question:
Do I need to any .cpt file ? (Because I have set Continuation=yes)

Thanks in advance






On Mon, May 2, 2011 at 3:27 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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