Chris: you're right man, let me be more concise.
Here there is the execution line I used: mpiexec -n $NSLOTS mdrun_mpi -np 1 -v -s start_res.tpr -o output_res -c output_conf -pi pull.ppa -pn mdgrp1.ndx -po pullout -pdo pullout1 * As for the pull.ppa file, here you go: ; GENERAL verbose = no Skip steps = 1 ; Runtype: afm, constraint, umbrella runtype = constraint ; Groups to be pulled group_1 = protein_a ; The group for the reaction force. reference_group = protein_b ; Weights for all atoms in each group (default all 1) weights_1 = weights_2 = weights_3 = weights_4 = reference_weights = ; Ref. type: com, com_t0, dynamic, dynamic_t0 reftype = com_t0 ; Use running average for reflag steps for com calculation reflag = 1 ; Select components for the pull vector. default: Y Y Y pulldim = Y Y Y ; DYNAMIC REFERENCE GROUP OPTIONS ; Cylinder radius for dynamic reaction force groups (nm) r = 1 ; Switch from r to rc in case of dynamic reaction force rc = 1.2 ; Update frequency for dynamic reference groups (steps) update = 1 ; CONSTRAINT RUN OPTIONS ; Direction, default: 0 0 0, no direction constraint_direction = 1.0 1.0 1.0 ; Rate of chance of the constraint length, in nm/ps ;constraint_rate = 0.0 ; Tolerance of constraints, in nm constraint_tolerance = 1e-06 Thank you for your patience. Giuseppe PS: I used the correct files to start the run again and I also visualized the configurations: thus, the pulled protein has moved for real (while it should be stuck at the initial point!). 2010/1/24 <chris.ne...@utoronto.ca> > Dear Giuseppe: > > I don't think your method of showing the change is very good since it > introduces unnecessary variables (e.g. did you use the correct files for the > second run). > > What I am looking for is raw -pd pull.pdo data from the first run. I found > no such file in the body of the email and I subscribe to get coallated lists > so I never get email attachments (and wouldn't open them even if I did). > > It looks to me like what you attached is part of mdout.mdp or perhaps -po > pullout.ppa. > > 3.3.3 mdrun -h says: > > -pi pull.ppa Input, Opt. Pull parameters > -po pullout.ppa Output, Opt. Pull parameters > -pd pull.pdo Output, Opt. Pull data output > -pn pull.ndx Input, Opt. Index file > > -- original message -- > > Hi Chris, > > the pdo file was attached at the bottom of my previous e-mail. As for > the output, you may read the information about the COMs in the md.log > file. Here there is an extended portion of it at the beginning of the > simulation: > > ************************************************** > PULL INFO > ************************************************** > RUN TYPE: Constraint > REFERENCE TYPE: center of mass of reference group at t=0 > Looking for group protein_a: found group protein_a: 1323 elements. First: 1 > Looking for group protein_b: found group protein_b: 1323 elements. First: > 1324 > Initializing pull groups. Inv. mass of group 1: 0.000070 > Initial coordinates center of mass: 3.100 2.983 3.377 > Initializing reference group. Inv. mass: 0.000070 > Initial coordinates center of mass: 2.972 3.006 8.821 > > Constraining the starting coordinates (step -2) > > > And here the same at the beginning of another simulation continuing > from the previous one (duration 1.5 ns): > > ************************************************** > PULL INFO > ************************************************** > RUN TYPE: Constraint > REFERENCE TYPE: center of mass of reference group at t=0 > Looking for group protein_a: found group protein_a: 1323 elements. First: 1 > Looking for group protein_b: found group protein_b: 1323 elements. First: > 1324 > Initializing pull groups. Inv. mass of group 1: 0.000070 > Initial coordinates center of mass: 3.040 3.690 2.740 > Initializing reference group. Inv. mass: 0.000070 > Initial coordinates center of mass: 2.976 3.005 8.828 > > Constraining the starting coordinates (step -2). > > > Let me know what you think, thanks. > > Giuseppe > > > 2010/1/24 <chris.ne...@utoronto.ca> > > [Hide Quoted Text] > Please provide actual gromacs output and tell us where it is from. I know > it's sad, but not all of us can recall what the gromacs 3.3.3 .pdo file > format looked like. So please include a sufficiently large portion of the > file to help us recall. If, on the other hand, these values that you place > below are from some other tool, then let us know the details about that. > > <snip> > > > -- > 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/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
-- 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/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/mailing_lists/users.php