[gmx-users] Umberella sampling

Justin A. Lemkul jalemkul at vt.edu
Sun May 8 17:00:48 CEST 2011

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 

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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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