[gmx-users] LINCS constraint on DU-DU bond

[Luirink, R.A.]

Sure, was planning to indeed. In the topology file ffnonbonded.itp I gave the new atom type atom number 1, such that I could constrain it together with all the hydrogens.
Rosa

On 14/12/2019, 01:52, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Justin Lemkul" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of jalemkul at vt.edu> wrote:

    
    
    On 12/13/19 9:43 AM, Luirink, R.A. wrote:
    > I found the solution!
    
    Please post the solution so that others can benefit in the future.
    
    -Justin
    
    >
    > On 13/12/2019, 13:53, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, R.A." <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of r.a.luirink at vu.nl> wrote:
    >
    >      Hi,
    >      I would like to constrain a bond between two dummy atoms using LINCS constraints. As I want to perturb the atoms towards a N-H bond, I would like to pre-treat it as such, due to the low mass of one of the dummy atoms.
    >      Is this possible somehow? And, if not, how is the constraint introduced during the perturbation from DU to H atom?
    >      (using gromacs version 2018.6)
    >      Thanks in advance,
    >      Rosa
    >      --
    >      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-request at gromacs.org.
    >      
    >
    
    -- 
    ==================================================
    
    Justin A. Lemkul, Ph.D.
    Assistant Professor
    Office: 301 Fralin Hall
    Lab: 303 Engel Hall
    
    Virginia Tech Department of Biochemistry
    340 West Campus Dr.
    Blacksburg, VA 24061
    
    jalemkul at vt.edu | (540) 231-3129
    http://www.thelemkullab.com
    
    ==================================================
    
    -- 
    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-request at gromacs.org.