[gmx-users] dihedral restraints in v3.3 different than v3.3.1 (or broken)
This is just a notice for the archives. I was recently working on a new cluster where only gromacs 3.3 is installed. It took me a while to figure out that the [ dihedral_restraints ] section is either differently implemented or broken in 3.3 compared to 3.3.1. Since the online list of revisions is not up to date past 3.2, I thought I would put a note on the mailing list. There is some discussion about versions and dihedral restraints here: http://www.gromacs.org/pipermail/gmx-users/2006-March/020512.html And for using dihedral restraints in 3.3.1, a description is here: http://www.gromacs.org/pipermail/gmx-users/2006-December/025087.html ___ 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] energy minimization breaks freeze group apart
I want to do energy minimization on a loop that had been missing and was filled in by modloop, while freezing the rest of the protein. Before the minimization I have an SO4 ion and 135 water molecules from the crystallography around the protein. After the minimization the protein has been translated in the y direction away from the water and SO4. My freeze group is : 0 & ! 15 which is System and not loop. I’m confused about why part of the freeze group (the protein) is translated away from the other part (So4 + crystal water). This happens with both steep and l-bfgs. Thanks for your help! Patricia Francis-Lyon _ Shed those extra pounds with MSN and The Biggest Loser! http://biggestloser.msn.com/___ 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
Re: [gmx-users] problem regarding editconf
> hi all, > i have one problem regarding 'editconf' for using add simulation box, my > protein contain 59 residues + crystal water -103 molecules > In one tutorial they have used following command for add simualation box > 1.editconf bt cubic f fws.pdb o fws.pdb d 0.9- in this 0.9 is nm Please be accurate. The above command line was not what the tutorial will have had - rather "editconf -bt cubic" etc. > i have reffered in gmxusers(archives) they have used following command > for > adding simulation box and water > 1. editconf -f popc128a.pdb -o po_box.pdb -box 6.1065 6.1059 9. -c > 2. genbox -cp po_box.pdb -cs -o po_sol.pdb -p lip.top > > based on above things i have used following commands for adding simulation > box and water > > 1.editconf bt cubic f fws.pdb o fws.pdb d 0.4- in this 0.4 is nm Using the same file name for input and output is asking for trouble. > 2. genbox -cp po_box.pdb -cs -o po_sol.pdb -p prot.top > program was finished without error and it added 4884 water molecules > around > my protein > is it right, what i have done or any chages i have to do? That depends what you want the simulation to do. 0.4nm margins are so small that your periodic copies will be interacting with each other. This is unrealistic. Check out some textbook material here. 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] problem regarding editconf
hi all, i have one problem regarding 'editconf' for using add simulation box, my protein contain 59 residues + crystal water -103 molecules In one tutorial they have used following command for add simualation box 1.editconf bt cubic –f fws.pdb –o fws.pdb –d 0.9- in this 0.9 is nm i have reffered in gmxusers(archives) they have used following command for adding simulation box and water 1. editconf -f popc128a.pdb -o po_box.pdb -box 6.1065 6.1059 9. -c 2. genbox -cp po_box.pdb -cs -o po_sol.pdb -p lip.top based on above things i have used following commands for adding simulation box and water 1.editconf bt cubic –f fws.pdb –o fws.pdb –d 0.4- in this 0.4 is nm 2. genbox -cp po_box.pdb -cs -o po_sol.pdb -p prot.top program was finished without error and it added 4884 water molecules around my protein is it right, what i have done or any chages i have to do? pls help me. thanks in advance. ___ 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] ask help for Potential energy curve calculation
Dear all, Now I need use GROMACS/CPMD to calculate the potential energy curve for a molecular solved in liquid. Please see the related content of the CPMD_inp.tmpl and the output for the details. $ cat em.mdp title = AU cpp = /usr/bin/cpp constraints = all-bonds constraint_algorithm= shake integrator = steep nsteps = 50 ... QMMM= yes QMmethod= CPMD QMMMscheme = normal QMMM-grps = QM QMbasis = STO-3G planewavecutoff = 25 qmmmcoul_cutoff = 25 MMlayer_radii = 10 10 MMlayer_updfqs = 1 1 ; box for cpmd run in a.u. qmbox_cpmd = 40. 30. 30. $ head -7 CPMD_inp.tmpl &CPMD INTERFACE GMX PCGFIRST PCG MINIMIZE MOLECULE CENTER OFF OPTIMIZE WAVEFUNCTION &END $ cat output.em THE FOLLOWING OPTIONS ARE MUTUALLY EXCLUSIVE MOLECULAR DYNAMICS GEOMETRY OPTIMIZATION WAVEFUNCTION OPTIMIZATION KOHN-SHAM ENERGIES VIBRATIONAL ANALYSIS PROPERTIES ORBITAL HARDNESS ELECTRONIC SPECTRA DEBUG FORCES LINEAR RESPONSE CLASSICAL INTERFACE PROGRAM STOPS IN SUBROUTINE CONTROL| RUNOPTIONS Would anyone tell me how I can calculte potential energy curve with Gromacs/CPMD if the interface GMX and the OPTIMIZE option cannot be used at the same time? Thank you so much. Best regards, Yun-an ___ 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
