[gmx-users] CONSTRAINED SIMULATIONS
Giuseppe Pellicane
gpellicane at unime.it
Sun Jan 24 18:34:58 CET 2010
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>
> 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
>
> * Previous message: [gmx-users] simulation crash with GROMOS96 force
> field
> * Next message: [gmx-users] Re: gas adsorption on CNT
> * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>
> 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
>
>
> --
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