[gmx-users] Justin umbrella sampling tutorial......

Justin A. Lemkul jalemkul at vt.edu
Thu May 24 07:20:27 CEST 2012

On 5/24/12 7:11 AM, rama david wrote:
> Thank you justin..
> I solve script problem..
>   I have another query ..
>   As mention in tutorial , In step six , we have to do brief NPT equilibration
>   npt_umbrella.mdp link is
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/npt_umbrella.mdp
>   After these we have to run MD ...mdp file link is
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_umbrella.mdp
> 1.  In both case define is same..
>       In general When we are doing NPT we are position restrain whole protein
> backbone ,
>       But in these case we are only restrain chain B...Please explain in detail ...

Please read the paper we published using this system.  It explains the 
conceptual details.

> 2.  The difference in mdp file is at gen_vel, and  run time 100 ps for  npt , 10
> ns for  md
>        If both mdp file is same Then why to do separate npt and md
>       ( Is the only reason is to generate velocity in npt simulation ???  Why we
> are not using velocity from
>           pull /(step five)/   )
> 3 . If we are using the gen_vel = yes
>        continuation                = yes
>        If continuation is yes, then why gen_vel is yes ????
> Please shade some light on meaning of continuation and gen_vel

At this point, you're basically starting a new simulation in the absence of a 
net pull force.  You're using the umbrella potential as a restraint, not to bias 
the motion, so you're re-equilibrating.  The use of "continuation = yes" simply 
implies that the starting configuration has already been constrained and thus 
the constraints should not be reset.  In this context, the difference between 
"yes" and "no" is likely not particularly relevant.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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