Hi all, The new addUnknownAtoms function is very timely as it's exactly what I need. I did notice a problem with it, however. In the middle of the calculation, the program stop, claiming that it was missing an atom. I found that by decreasing the timestep, and increasing the number of steps, I could work around this problem.
I also copied some code from tutorial/tidbits/sidechainbuild.inp that should take care of the changing mass problem in addUnknownAtoms, though I haven't tested it yet. Patch including both changes is attached. One question - I think it would be useful to see the output of the minimization in addUnknownAtoms, but when I turn on the normal output, I get a huge number of %atom warnings about atoms being too close together. Is there a way to shut the %atom warnings off, but preserve the rest of the minimization output? -Greg Zornetzer [email protected] -------------- next part -------------- --- python/protocol.py.orig 2005-12-14 14:13:52.000000000 -0600 +++ python/protocol.py 2005-12-14 14:22:41.000000000 -0600 @@ -686,6 +686,7 @@ xplor.command(r""" vector do (fbeta=10) (not known) {*Friction coefficient for MD heatbath.*} +vector do (q=mass) (all) {* Save the real masses for later *} vector do (mass=100) (not known) {*Uniform heavy masses to speed*} vector do (fbeta=0) (known) {*Friction coefficient for MD heatbath.*} vector do (mass=0) (known) {*Uniform heavy masses to speed*} @@ -732,8 +733,8 @@ evaluate ($kbon = 0.00005 ) {* Bonds. *} evaluate ($kang = 0.00005 ) {* Angles. *} - evaluate ($timestep = 0.04) - evaluate ($nstep = 100) + evaluate ($timestep = 0.004) + evaluate ($nstep = 1000) !constraints ! interaction (all) (all) @@ -789,7 +790,7 @@ weights bond $kbon angl $kang impr $kimp vdw 0.002 elec 0 end end dynamics verlet - nstep=500 timestep=$timestep iasvel=current + nstep=5000 timestep=$timestep iasvel=current tcoupling=true tbath=$init_t nprint=50 iprfrq=0 end constraints @@ -799,7 +800,7 @@ weights bond $kbon angl $kang impr $kimp vdw 0.005 elec 0 end end dynamics verlet - nstep=500 timestep=$timestep iasvel=current + nstep=5000 timestep=$timestep iasvel=current tcoupling=true tbath=$init_t nprint=50 iprfrq=0 end constraints @@ -809,7 +810,7 @@ weights bond $kbon angl $kang impr $kimp vdw 0.01 elec 0 end end dynamics verlet - nstep=500 timestep=$timestep iasvel=current + nstep=5000 timestep=$timestep iasvel=current tcoupling=true tbath=$init_t nprint=50 iprfrq=0 end constraints @@ -819,7 +820,7 @@ weights bond $kbon angl $kang impr $kimp vdw 0.5 elec 0 end end dynamics verlet - nstep=500 timestep=$timestep iasvel=current + nstep=5000 timestep=$timestep iasvel=current tcoupling=true tbath=$init_t nprint=50 iprfrq=0 end @@ -844,8 +845,12 @@ drop=100 nprint=1 tolg=1e-5 - nstep=10000 -end""") + nstep=10000 +end + +vector do (mass=q) (all) {* Return the masses to sane values *} + +""") xplor.command("set mess=%s print=OUTPUT echo=%s end"%(old_mess,old_echo)) return
