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:
[EMAIL PROTECTED] 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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