[gmx-users] CONSTRAINED SIMULATIONS

[Giuseppe Pellicane]

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.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>
>
>
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