Re: [gmx-users] Distance constrained energy minimization and MD
jayant james wrote: Hi all! The protein that I am trying to simulate has 3 chains. My aim is to apply harmonic constraints to certain parts of the protein and (based on FRET derived distances) I am attempting to incorporate distance constraint between certain amino acids of different chains during EM and MD. Constraints and restraints are different concepts in GROMACS. Look them up in the manual. _Harmonic Constraints_ I figured, that for the harmonic constraining the input is in the file "posres_D.itp" and I specify define = -DFLEXIBLE -DPOSRES in the em.mdp _Distance constraints _ I would also like to have amino acids contrained, not by a fixed distance but within a range(say 45-75 angstroms). How do I go about doing this? Check out distance restraints in the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Distance constrained energy minimization and MD
Hi all! The protein that I am trying to simulate has 3 chains. My aim is to apply harmonic constraints to certain parts of the protein and (based on FRET derived distances) I am attempting to incorporate distance constraint between certain amino acids of different chains during EM and MD. *Harmonic Constraints* I figured, that for the harmonic constraining the input is in the file "posres_D.itp" and I specify define = -DFLEXIBLE -DPOSRES in the em.mdp *Distance constraints * I would also like to have amino acids contrained, not by a fixed distance but within a range(say 45-75 angstroms). How do I go about doing this? thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
