[gmx-users] CONSTRAINED SIMULATIONS

[chris.neale at 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.neale at 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>