Thank you very much Justin. Here it is working but having some problem. pull_group2_name = chain_B35 is moving in the + z direction & pull_group4_name= chain_B26 is moving oppositely in the -z direction While I have given pull in +z direction for both the above group.
Note - pull_group1_name = chain_A8 and pull_group3_name = chain_A17 are immobile here as well as acting as reference. On Thu, Feb 1, 2018 at 7:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/1/18 7:59 AM, Rakesh Mishra wrote: > >> Dear Justin >> >> Here I am applying pull for two groups with respect to two reference group >> as following. >> ; Pull code >> pull = yes >> pull_ngroups = 4 >> pull_ncoords = 1 >> pull_group1_name = chain_A8 (reference also immobile ) >> pull_group2_name = chain_B35 (pulling group) >> pull_group3_name = chain_A17 (reference also immobile) >> pull_group4_name = chain_B26 (pulling) >> pull_coord1_type = umbrella ; harmonic biasing force >> pull_coord1_geometry = distance ; simple distance increase >> pull_coord1_groups = 1 2 >> pull_coord1_dim = N N Y >> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per 1 ns >> pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 >> pull_coord1_start = yes ; define initial COM distance > 0 >> >> In above protocol I want to make two reference group as >> 1-chain_A8 2- chain_A17 >> and two pull group. >> 1- chain_B35 2- chain_B26 >> > > You've defined four groups but then only used two, so you only get the > effect of one reaction coordinate. > > What you need to do is define the pull settings for all reaction > coordinates simultaneously, e.g.: > > pull = yes > pull_ngroups = 4 > pull_ncoords = 2 > pull_group1_name = chain_A8 > pull_group2_name = chain_B35 > pull_group3_name = chain_A17 > pull_group4_name = chain_B26 > ; definition of reaction coordinate 1, groups 1-2 > pull_coord1_type = umbrella > pull_coord1_geometry = distance > pull_coord1_groups = 1 2 > pull_coord1_dim = N N Y > pull_coord1_rate = 0.01 > pull_coord1_k = 1000 > pull_coord1_start = yes > ; definition of reaction coordinate 2, groups 3-4 > pull_coord2_type = umbrella > pull_coord2_geometry = distance > pull_coord2_groups = 3 4 > pull_coord2_dim = N N Y > pull_coord2_rate = 0.01 > pull_coord2_k = 1000 > pull_coord2_start = yes > > Note that above I changed pull_ncoords to be set to 2, because you want > two reaction coordinates. Then just specify the settings for each one, > calling the appropriate groups by their assigned numbers. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > 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. > -- * 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.