[gmx-users] Test Particle Insertion

Phan, Anh T. anhphan at ou.edu
Thu Jun 20 21:08:43 CEST 2013

Dear GMX Users,
My name is Anh Phan, a PhD student at University of Oklahoma.
I would like to calculate excess chemical potential of one gas molecule in water solvent using Widom test particle insertion with Gromacs.
In this method, I will insert this gas molecule at a random position in each configuration of the system.
With Gromacs, I see I can use tpi (integrator = tpi).
I know I have to add this gas molecule in the topology (topol.top)
Also, it is indicated in the manual that insertions are performed nsteps times in each frame at random locations and with random orientiations of the molecule. That is what I desire.
The question I would like to ask is whether I have to add the specified coordinate of gas molecule in the .gro file at the beginning of running simulation.
For example, in the initial.gro file
26734SOL     OW45744  21.969   6.237   2.921
26734SOL    HW145745  21.969   6.253   3.019
26734SOL    HW245746  21.886   6.188   2.895
26735SOL     OW45747  15.155   7.211   2.853
26735SOL    HW145748  15.220   7.265   2.801
26735SOL    HW245749  15.204   7.151   2.916
26736SOL     OW45750  24.606   4.896   3.053
26736SOL    HW145751  24.594   4.972   2.989
26736SOL    HW245752  24.532   4.896   3.120
26737INS             X45752        1.000        1.000        1.000 ( Do I have to add this line in the initial.gro file)

The command lines
grompp -f input.mdp -c initial.gro -p topol.top -n index.ndx -o tpi.tpr -maxwarn 2
mdrun -s tpi.tpr -rerun md.trr -x traj.xtc -c final.gro -e init3.ener -g init3.log -deffnm tpi -tpi tpi.xvg -tpid tpid.xvg

I am looking forward to receiving your reply.
Thank you for your help.

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