[gmx-users] AFM Pulling

[Arneh Babakhani]

Hi all, nevermind, I caught my own mistake.  (I hope this might be 
useful for someone in the future).

PeptidePull.ppa is my input file, specifying the parameters for my 
pulling. 

-po PeptidePull is the output file.  The problem here is that I used the 
same name.

When it crossed over to another node, the wrong ppa file was read. 

So the moral of the story is: When running AFM pulling in parallel, make 
sure that the names following "-pi" and "-po" differ!  (something like, 
"-pi PeptidePull -po ExtraPeptidePull).

Thanks!

Arneh



Arneh Babakhani wrote:
>> 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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