GROMACS version: 2020.7
GROMACS modification: No
I am currently trying to pull a box in X-direction with these settings in my mdp
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 = -1 ; 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 motion. 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.