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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