[gmx-users] Umberella sampling

[mohsen ramezanpour]

Thank you very much
I understood completely
Best

On Sun, May 8, 2011 at 7:30 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> Thank you for your complete explanation.
>> Please let me discribe  where is NPT.cpt  comes from:
>>
>> Before doing Pulling step,I did an NPT step (as your tutorial) to generate
>> NPT ensemble.
>> the outputs of this step were NPT.cpt,  NPT.gro and NPT.enr and ...
>>
>> Then I used NPT.gro for Pulling step to generate config0.gro and ...
>>
>> After this step I used the NPT.cpt  and  config0.gro and .... to generate
>> umbrella0.tpr with  grompp.
>> I think it is obvious now ,where is  NPT.cpt  come from!
>>
>> I think my mistake is as you noted.I didn't use any  -t option in
>> grompp,Then I lost the information for npt ensemble.
>>
>> What do you think
>>
>
> The pre-SMD NPT ensemble has nothing to do with any of the configurations
> generated during SMD.  The coordinates and ensemble information in NPT.cpt
> reflect the position-restrained system prior to the application of the
> steering force.
>
> You should not use this NPT.cpt file for anything after SMD.  I explained
> an appropriate workflow in my last message.
>
>
> -Justin
>
> --
> ========================================
>
> 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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