Dear Justin, Can you explain something regarding this issue.
I couldn't get resolve one problem. Though now I am able to make restrict (immobile ) the needed residue and pulled another one. But the contradiction that i am facing is that, when I am pulling with -rate (in negative z direction, as I want to pull the residue in the negative Z direction of box ) given below. Still there we see that pulling group is not moving the -ve direction of z. pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name = chain-A-start pull_group2_name = chain-B-end 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 per 1 ns pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 Best On Tue, Feb 6, 2018 at 1:54 PM, Rakesh Mishra <rockin...@gmail.com> wrote: > 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 <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.