________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Anik Sen [anik...@csmcri.org] Sent: Wednesday, June 20, 2012 8:24 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: RE: [gmx-users] to know about constraints
Hello Justin For freezefprs, am using the .mdp file as follows: ; title = NACL6 cpp = /usr/bin/cpp define = -DPOSRE constraints = none integrator = steep freezegrps = K+ CL- freezedim = N N ................................................. ................................................ The error file is coming as: Fatal error: Invalid Freezing input: 2 groups and 2 freeze values Is the .mdp wrong please suggest Specify index file which include those two groups (K+ C-) with those names. You should also specify the third dimension for each group I guess: freezedim = N N Y N N Y ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, June 20, 2012 12:09 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] to know about constraints On 6/19/12 2:35 PM, Anik Sen wrote: > Hello Justin, > This is Anik again. > I checked the links. But could not understand fully. Am giving the part of > the topology file as given below, generated with the command > > "pdb2gmx -f a.pdb -o b.pdb -p topol.top" > > The topology file : > > > " 205 CL- 205 CL- Cl 205 -1 35.453 ; qtot > 35 > 206 CL- 206 CL- Cl 206 -1 35.453 ; qtot > 34 > 207 CL- 207 CL- Cl 207 -1 35.453 ; qtot > 33 > 208 CL- 208 CL- Cl 208 -1 35.453 ; qtot > 32 > 209 CL- 209 CL- Cl 209 -1 35.453 ; qtot > 31 > 210 CL- 210 CL- Cl 210 -1 35.453 ; qtot > 30 > 211 CL- 211 CL- Cl 211 -1 35.453 ; qtot > 29 > 212 CL- 212 CL- Cl 212 -1 35.453 ; qtot > 28 > 213 CL- 213 CL- Cl 213 -1 35.453 ; qtot > 27 > 214 CL- 214 CL- Cl 214 -1 35.453 ; qtot > 26 > 215 CL- 215 CL- Cl 215 -1 35.453 ; qtot > 25 > 216 CL- 216 CL- Cl 216 -1 35.453 ; qtot > 24 > 217 CL- 217 CL- Cl 217 -1 35.453 ; qtot > 23 > 218 CL- 218 CL- Cl 218 -1 35.453 ; qtot > 22 > 219 CL- 219 CL- Cl 219 -1 35.453 ; qtot > 21 > 220 CL- 220 CL- Cl 220 -1 35.453 ; qtot > 20 > 221 CL- 221 CL- Cl 221 -1 35.453 ; qtot > 19 > 222 CL- 222 CL- Cl 222 -1 35.453 ; qtot > 18 > 223 CL- 223 CL- Cl 223 -1 35.453 ; qtot > 17 > 224 CL- 224 CL- Cl 224 -1 35.453 ; qtot > 16 > 225 CL- 225 CL- Cl 225 -1 35.453 ; qtot > 15 > 226 CL- 226 CL- Cl 226 -1 35.453 ; qtot > 14 > 227 CL- 227 CL- Cl 227 -1 35.453 ; qtot > 13 > 228 CL- 228 CL- Cl 228 -1 35.453 ; qtot > 12 > 229 CL- 229 CL- Cl 229 -1 35.453 ; qtot > 11 > 230 CL- 230 CL- Cl 230 -1 35.453 ; qtot > 10 > 231 CL- 231 CL- Cl 231 -1 35.453 ; qtot > 9 > 232 CL- 232 CL- Cl 232 -1 35.453 ; qtot > 8 > 233 CL- 233 CL- Cl 233 -1 35.453 ; qtot > 7 > 234 CL- 234 CL- Cl 234 -1 35.453 ; qtot > 6 > 235 CL- 235 CL- Cl 235 -1 35.453 ; qtot > 5 > 236 CL- 236 CL- Cl 236 -1 35.453 ; qtot > 4 > 237 CL- 237 CL- Cl 237 -1 35.453 ; qtot > 3 > 238 CL- 238 CL- Cl 238 -1 35.453 ; qtot > 2 > 239 CL- 239 CL- Cl 239 -1 35.453 ; qtot > 1 > 240 CL- 240 CL- Cl 240 -1 35.453 ; qtot > 0 > > ; Include Position restraint file > #ifdef POSRES > #include "posre.itp" > #endif > > ; Include water topology > #include "tip4p.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif " > > This includes the posre.itp as follows: > > " ; In this topology include file, you will find position restraint > ; entries for all the heavy atoms in your original pdb file. > ; This means that all the protons which were added by pdb2gmx are > ; not restrained. > > [ position_restraints ] > ; atom type fx fy fz > 215 1 1000 1000 1000 > 216 1 1000 1000 1000 > 217 1 1000 1000 1000 > 218 1 1000 1000 1000 > 219 1 1000 1000 1000 > 220 1 1000 1000 1000 > 221 1 1000 1000 1000 > 222 1 1000 1000 1000 > 223 1 1000 1000 1000 > 224 1 1000 1000 1000 > 225 1 1000 1000 1000 > 226 1 1000 1000 1000 > 227 1 1000 1000 1000 > 228 1 1000 1000 1000 > 229 1 1000 1000 1000 > 230 1 1000 1000 1000 > 231 1 1000 1000 1000 > 232 1 1000 1000 1000 > 233 1 1000 1000 1000 > 234 1 1000 1000 1000 > 235 1 1000 1000 1000 > 236 1 1000 1000 1000 > 237 1 1000 1000 1000 > 238 1 1000 1000 1000 > 239 1 1000 1000 1000 > 240 1 1000 1000 1000 " > > Now are these atoms already restrained, or we have to restrain tem by othr > means.. Provided that all of those atoms are in the same [moleculetype] in the topology, this is a correct approach. > As after the minimisation step, the atoms are moving from their positions, > which i donot want. > Did you set the correct "define" statement in the .mdp file? Also note that a position restraint does not completely prevent motion, it just disfavors it. The magnitude of the energy penalty for displacement depends on the force constant set in posre.itp. You can also use freezegrps to completely immobilize any subset of atoms in the system. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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 -- 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? 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