On 2012-09-29 12:42:29AM -0700, Acoot Brett wrote: > Dear All, > > I just run a grompp command "grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p > topol.top -o npt.tpr". It gives the following message, > > Generated 2211 of the 2211 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 2211 of the 2211 1-4 parameter combinations > Excluding 3 bonded neighbours molecule type 'Protein_chain_A' > turning all bonds into constraints... > Excluding 3 bonded neighbours molecule type 'Protein_chain_B' > turning all bonds into constraints... > Excluding 2 bonded neighbours molecule type 'SOL' > turning all bonds into constraints... > Excluding 1 bonded neighbours molecule type 'NA' > turning all bonds into constraints... > Excluding 1 bonded neighbours molecule type 'CL' > > Will you please tell me why grompp "exclude" and "turning"? What are their > functions? Based on what grompp process "exclude" and "turning"? > > I am looking forward to getting your reply.
Turning refers to turning bonds into constraints are defined in the .mdp file: constraints = whatever you have defined here (probably all-bonds if grompp is reporting that all bonds are turned into constraints) neighbor exclusions are from the beginning of the topology file for that particular [ moleculetype ] in the nrexcl field [ moleculetype ] ; name nrexcl Protein_chain_A 3 nonbonded interactions between atoms that are no further than nrexcl bonds away are excluded. See also http://lists.gromacs.org/pipermail/gmx-users/2011-May/061072.html -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
