[gmx-users] AFM Pulling

[Arneh Babakhani]

> Hi GXM Users,
>
> I'm trying to execute some AFM pulling.  My index file contains two 
> groups, [TopPeptide]  and [DMPC].   I execute grompp, then when I try 
> to execute mdrun:
>
> *[ababakha at chemcca50 SteeredMD]$ mdrun -s SMD-01.tpr -o SMD-01 -c 
> AfterSMD-01 -e SMD-01 -g SMD-01 -pi PeptidePull.ppa -pn System.ndx -po 
> PeptidePull -pdo PeptidePull *
>
> I get a prompt, asking me to select groups:
>
> *Back Off! I just backed up SMD-01.edr to ./#SMD-01.edr.3#
> Group     0 (  TopPeptide) has    72 elements
> Group     1 (        DMPC) has  5888 elements
> Select a group: 0 *
>
> My question is:  If I've already specified the group and the reference 
> group (in the PeptidePull.ppa file, which I've pasted below for your 
> reference) and if these groups are defined in the System.ndx file, 
> then why am I being prompted to select a group???  (incidently, when I 
> do select a group, I get several warnings that state "Unkown left-hand 
> afm_rate (or afm_k1, or afm_direction, etc etc) in parameter file".  
> Seems like it's not reading my PeptidePull.ppa file correctly).
>
> Would greatly appreciate any assistance,
>
> Arneh
>
> ; GENERAL               verbose                  = no
> Skip steps               = 1
> ; Runtype: afm, constraint, umbrella
> runtype                  = afm
> ; Number of pull groups
> ngroups                  = 1
> ; Groups to be pulled   group_1                  = TopPeptide
> ; The group for the reaction force.
> reference_group          = DMPC
> ; Weights for all atoms in each group (default all 1)
> weights_1                =
> reference_weights        =
> ; Ref. type: com, com_t0, dynamic, dynamic_t0
> reftype                  = com_t0
> ; Use running average for reflag steps for com calculation
> reflag                   = 10
> ; Select components for the pull vector. default: Y Y Y
> pulldim                  = N N Y
> ; DYNAMIC REFERENCE GROUP OPTIONS
> ; Cylinder radius for dynamic reaction force groups (nm)
> r                        = 0
> ; Switch from r to rc in case of dynamic reaction force
> rc                       = 0
> ; Update frequency for dynamic reference groups (steps)
> update                   = 1
>
> ; CONSTRAINT RUN OPTIONS
> ; Direction, default: 0 0 0, no direction
> constraint_direction     = 0.0 0.0 0.0
> ; Constraint distance (nm), default: 0, use starting distance
> constraint_distance1     = 0
> ; Rate of chance of the constraint length, in nm/ps
> constraint_rate1         = 0
> ; Tolerance of constraints, in nm
> constraint_tolerance     = 1e-06
>
> ; AFM OPTIONS          ; Pull rates in nm/ps   
> afm_rate1                = 0.0064
> ; Force constants in kJ/(mol*nm^2)
> afm_k1                   = 500
> ; Directions            afm_dir1                 = 0 0 -1
> ; Initial spring positions
> afm_init1                = 0.40434290838 0.41850681958 3.19817446605
>
> ; UMBRELLA SAMPLING OPTIONS
> ; Force constants for umbrella sampling in kJ/(mol*nm^2)
> ; Centers of umbrella potentials with respect to reference:
> ; Ref - Pull.           K1                       = 0
> Pos1                     = 0.0 0.0 0.0
>
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