From: Udaya Dahal (dahal.udaya_at_gmail.com)
Date: Tue Oct 16 2018 - 19:08:07 CDT
Hi Everyone,
I am trying to calculate PMF for a peptide chain bound to surface. I have a
fixed surface and the reaction coordinate is along z-direction. For
umbrella sampling, I need to restrain my peptide's center of mass at
specific point along z direction. For this I used one (fixed atom) from
surface as a reference atom and peptides atoms as group of atoms for
"distanceZ" module in namd, The script is as follows similar to that in the
tutorial. The following description doesn't seem to define center of mass
of the atoms for the "main" which led to crashing the simulation( my
assumption). The "distance" module seems defines two center of mass groups
but there is no option for restraining along particular axis. I would
appreciate if there is any suggestion on how to proceed from here.
colvar {
name Translocation
width 0.1
lowerboundary 40.0
upperboundary 100.0
lowerwallconstant 100.0
upperwallconstant 100.0
distanceZ {
main {
atomnumbers { 7301 7302 7303 7304 7305 7306 7307 7308 7309 7310
7311 7312 7313 7314 7315 7316 7317 7318 7319 7320 7321 7322 7323 7324 7325
7326 7327 7328 7329 7330 7331 7332 7333 7334 7335 7336 7337 7338 7339 7340
7341 7342 7343 7344 7345 7346 7347 7348 7349 7350 7351 7352 7353 7354 7355
7356 7357 7358 7359 7360 7361 7362 7363 7364 7365 7366 7367 7368 7369 7370
7371 7372 7373 7374 7375 7376 7377 7378 7379 7380 7381 7382 7383 7384 7385
7386 7387 7388 7389 7390 7391 7392 7393 7394 7395 7396 7397 7398 7399
}
}
ref {
atomnumbers { 1910
}
}
axis ( 0.0, 0.0, 1.0 )
}
}
harmonic {
name Z
colvars Translocation
CENTER 11.5
forceConstant 0.025
}
Regards,
Udaya
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