[gmx-users] Test Particle Insertion

[João M. Damas]

Dear Anh,

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).

Best,
João


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
> 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.
> Sincerely,
> Anh
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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613