[gmx-users] Justin umbrella sampling tutorial......
ramadavidgroup at gmail.com
Thu May 24 07:11:35 CEST 2012
Thank you justin..
I solve script problem..
I have another query ..
As mention in tutorial , In step six , we have to do brief NPT
npt_umbrella.mdp link is
After these we have to run MD ...mdp file link is
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
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,
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