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

rama david 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
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120524/afa0273b/attachment.html>

More information about the gromacs.org_gmx-users mailing list