[gmx-users] CONSTRAINED SIMULATIONS

[chris.neale at utoronto.ca]

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.

-- original message --

Hello,

I'm trying to do constrained simulations of a system consisting of two
solvated proteins separated at a given distance. Inside the box there are
also
around 14.000 water molecules. At the bottom there is the .pdo
file (I'm using gromacs 3.3.3).

However, it seems as it does not work. At the beginning of a simulation of
1.5 ns
this was the positions of the centers of mass of the two proteins:

Initial coordinates center of mass:    3.100    2.983    3.377
Initial coordinates center of mass:    2.972    3.006    8.821

After 1.5 ns:

Initial coordinates center of mass:    3.040    3.690    2.740
Initial coordinates center of mass:    2.976    3.005    8.828

The distance changed from 5.445 nm to 6.127 nm.
What's wrong?

I appreciate your advice on this issue. Thank you very much in advance,

Joseph


; 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
CONSTRAINED SIMULATIONS
Giuseppe Pellicane giuseppepellicane at gmail.com
Sun Jan 24 11:27:23 CET 2010

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Hello,

I'm trying to do constrained simulations of a system consisting of two
solvated proteins separated at a given distance. Inside the box there are
also
around 14.000 water molecules. At the bottom there is the .pdo
file (I'm using gromacs 3.3.3).

However, it seems as it does not work. At the beginning of a simulation of
1.5 ns
this was the positions of the centers of mass of the two proteins:

Initial coordinates center of mass:    3.100    2.983    3.377
Initial coordinates center of mass:    2.972    3.006    8.821

After 1.5 ns:

Initial coordinates center of mass:    3.040    3.690    2.740
Initial coordinates center of mass:    2.976    3.005    8.828

The distance changed from 5.445 nm to 6.127 nm.
What's wrong?

I appreciate your advice on this issue. Thank you very much in advance,

Joseph


; 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