Chris:<br><br>you're right man, let me be more concise.<br><br>Here there is the execution line I used:<br><br> 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 *<br>
<br>As for the pull.ppa file, here you go:<br><br>; GENERAL<br>verbose = no<br>Skip steps = 1<br>; Runtype: afm, constraint, umbrella<br>runtype = constraint<br>; Groups to be pulled<br>
group_1 = protein_a<br>; The group for the reaction force.<br>reference_group = protein_b<br>; Weights for all atoms in each group (default all 1)<br>weights_1 =<br>weights_2 =<br>
weights_3 =<br>weights_4 =<br>reference_weights =<br>; Ref. type: com, com_t0, dynamic, dynamic_t0<br>reftype = com_t0<br>; Use running average for reflag steps for com calculation<br>
reflag = 1<br>; Select components for the pull vector. default: Y Y Y<br>pulldim = Y Y Y<br>; DYNAMIC REFERENCE GROUP OPTIONS<br>; Cylinder radius for dynamic reaction force groups (nm)<br>
r = 1<br>; Switch from r to rc in case of dynamic reaction force<br>rc = 1.2<br>; Update frequency for dynamic reference groups (steps)<br>update = 1<br><br>; CONSTRAINT RUN OPTIONS<br>
; Direction, default: 0 0 0, no direction<br>constraint_direction = 1.0 1.0 1.0<br>; Rate of chance of the constraint length, in nm/ps<br>;constraint_rate = 0.0<br>; Tolerance of constraints, in nm<br>constraint_tolerance = 1e-06<br>
<br>Thank you for your patience.<br><br>Giuseppe <br><br>PS: I used the correct files to start the run again and I also visualized<br>the configurations: thus, the pulled protein has moved for real (while <br>it should be stuck at the initial point!).<br>
<br><div class="gmail_quote">2010/1/24 <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Giuseppe:<br>
<br>
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).<br>
<br>
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).<br>
<br>
It looks to me like what you attached is part of mdout.mdp or perhaps -po pullout.ppa.<br>
<br>
3.3.3 mdrun -h says:<br>
<br>
-pi pull.ppa Input, Opt. Pull parameters<br>
-po pullout.ppa Output, Opt. Pull parameters<br>
-pd pull.pdo Output, Opt. Pull data output<br>
-pn pull.ndx Input, Opt. Index file<br>
<br>
-- original message --<br>
<br>
Hi Chris,<br>
<br>
the pdo file was attached at the bottom of my previous e-mail. As for<br>
the output, you may read the information about the COMs in the md.log<br>
file. Here there is an extended portion of it at the beginning of the<br>
simulation:<br>
<br>
**************************************************<br>
PULL INFO<br>
**************************************************<br>
RUN TYPE: Constraint<br>
REFERENCE TYPE: center of mass of reference group at t=0<br>
Looking for group protein_a: found group protein_a: 1323 elements. First: 1<br>
Looking for group protein_b: found group protein_b: 1323 elements. First:<br>
1324<br>
Initializing pull groups. Inv. mass of group 1: 0.000070<br>
Initial coordinates center of mass: 3.100 2.983 3.377<br>
Initializing reference group. Inv. mass: 0.000070<br>
Initial coordinates center of mass: 2.972 3.006 8.821<br>
<br>
Constraining the starting coordinates (step -2)<br>
<br>
<br>
And here the same at the beginning of another simulation continuing<br>
from the previous one (duration 1.5 ns):<br>
<br>
**************************************************<br>
PULL INFO<br>
**************************************************<br>
RUN TYPE: Constraint<br>
REFERENCE TYPE: center of mass of reference group at t=0<br>
Looking for group protein_a: found group protein_a: 1323 elements. First: 1<br>
Looking for group protein_b: found group protein_b: 1323 elements. First:<br>
1324<br>
Initializing pull groups. Inv. mass of group 1: 0.000070<br>
Initial coordinates center of mass: 3.040 3.690 2.740<br>
Initializing reference group. Inv. mass: 0.000070<br>
Initial coordinates center of mass: 2.976 3.005 8.828<br>
<br>
Constraining the starting coordinates (step -2).<br>
<br>
<br>
Let me know what you think, thanks.<br>
<br>
Giuseppe<br>
<br>
<br>
2010/1/24 <<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a>><br>
<br>
[Hide Quoted Text]<br>
Please provide actual gromacs output and tell us where it is from. I know<br>
it's sad, but not all of us can recall what the gromacs 3.3.3 .pdo file<br>
format looked like. So please include a sufficiently large portion of the<br>
file to help us recall. If, on the other hand, these values that you place<br>
below are from some other tool, then let us know the details about that.<br>
<br>
<snip><br><font color="#888888">
<br>
<br>
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</font></blockquote></div><br>