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

[rama david]

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 ...

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


Thank you in advance


With Best Wishes,
Rama David
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