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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