[gmx-users] Umberella sampling
ramezanpour.mohsen at gmail.com
Sun May 8 17:07:30 CEST 2011
Thank you very much
I understood completely
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 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users