Thanks Justin I followed your suggestion. now I am able to restrain (immobile) any molecule during pulling.
thanks for your help. On Tue, Jan 2, 2018 at 4:56 PM, Rakesh Mishra <rockin...@gmail.com> wrote: > Dear all > > 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 <094736%2062491>, +91877749632* > -- * 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.