Dear sir I am just a beginner in gromacs. I have installed gromacs 5.1 version. I am doing pulling for si-rna (double stranded, 22 nucleotides each ). I am applying pulling code of umbrella sampling. Using that, we have chosen 22nd number residue of chain A is under pulling with constant velocity rate in +ve x direction. and residue 44 of apposite chain B at the apposite end is taking as reference . Now I am thinking to make the reference residue 44 as immobile. But when after simulation I am trying to see the trajectory . Then I Am finding that the residue n 44 (reference residue of pulling) is also moving and which is in apposite direction. even it is showing that reference residue 44 is crossing the box wall in -ve x direction.
My aim is to pull residue n 22 of chain-A of si-rna by making reference residue n 44 of chain-B of si-rnA as a immobile, i mean no need for big motion in apposite direction. -- * Rakesh Kumar Mishra* * (RA)CSD SINP Kolkata, India* *E-mail - rakesh.mis...@saha.ac.in <rakesh.mis...@saha.ac.in> * *Phone n. +91 9473662491, +91877749632* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.