[gmx-users] Test Particle Insertion
João M. Damas
jmdamas at itqb.unl.pt
Fri Jun 21 01:29:15 CEST 2013
You need to construct a .tpr file for the mdrun -rerun with:
- a .gro file with the ligand to be inserted at the end, which _must_ be
geometrically centered at 0,0,0 ;
- a matching .top file (which means with the ligand topology
appropriately inserted) ;
- a .mdp file with the specific parameters for the tpi algorithm .
Since you happen to have a single particle to insert, that particle's
coordinates should be 0,0,0 in the .gro file from grompp (your initial.gro).
On Thu, Jun 20, 2013 at 8:08 PM, Phan, Anh T. <anhphan at ou.edu> wrote:
> 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
> 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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João M. Damas
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
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