A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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# This file was created Tue Jun 7 16:54:27 2022
# Created by:
# :-) GROMACS - gmx msd, 2020.6-Debian-2020.6-2 (-:
#
# Executable: /usr/bin/gmx
# Data prefix: /usr
# Working dir: /home/student/adit/CMMDE_launching/larutan/SistemLarutan
# Command line:
# gmx msd -f nvep.trr -s nvep.tpr -n URA.ndx -o msd_URA.xvg
# gmx msd is part of G R O M A C S:
#
# Getting the Right Output Means no Artefacts in Calculating Stuff
#
@ title "Mean Square Displacement"
@ xaxis label "Time (ps)"
@ yaxis label "MSD (nm\S2\N)"
@TYPE xy
# MSD gathered over 5 ps with 1 restarts
# Diffusion constants fitted from time 0.5 to 4.5 ps
# D[(resname_URA)] = 12.3555 (+/- 8.7627) (1e-5 cm^2/s)
0 0
0.25 0.0133805
0.5 0.036392
0.75 0.0579278
1 0.0743596
1.25 0.0966733
1.5 0.112928
1.75 0.146919
2 0.181349
2.25 0.206685
2.5 0.223924
2.75 0.245809
3 0.259067
3.25 0.270479
3.5 0.277921
3.75 0.291355
4 0.295729
4.25 0.307507
4.5 0.322355
4.75 0.352738
5 0.400328