[gmx-users] compute displacement

leila separdar separdar.leila at gmail.com
Sun Jul 24 15:51:52 CEST 2011

I have performed a MD simulation with gromacs 4.0.7 the system that I
have simulated contain 1000 atomes and now in order to compute
intermediate scattering function
F(q,t)=1/N<∑_(i=1)^N〖exp⁡(-iq.(r_i (t)-r_(i(0))> I need to compute (ri
(t)-ri(0)) for all atomes and all times. how can I do this? mean
square of this term gives us mean square displacment and the gromacs
can do it by using g_msd is there any command that give us
.(ri(t)-ri(0)) and not mean squre of it?
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