Hi, I am currently trying to pull a box in X-direction with these settings in my mdp file of gromacs.
tcoupl = v-rescale
tc-grps = System
tau_t = 1.0
ref_t = 310
Pcoupl = parrinello-rahman
Pcoupltype = semiisotropic
tau_p = 12.0
compressibility = 0 3e-4
ref_p = 1 1
gen_vel = no
gen_temp = 310
gen_seed = 473529
; options for deform
deform = 3e-7 0 0 0 0 0
refcoord_scaling = com
Are these settings fine if I want to pull the box in X-direction with this deform rate of 3e-7 nm/ps? Also, since my molecule rotates/translates a lot, do I need to fix my molecule and pull it? Or, it’s fine to pull the box even if the molecule is performing these motions. Finally, if I want to pull the molecule in x-direction, is it necessary to have this molecule aligned at this particular direction at first, and have the box created with x and y length equal to the respective x and y length of the molecule so that the molecule just fits inside the box. BTW - I am doing a CG MD simulation. Thanks
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