As far as I know it should not be included. Make a tpr file new .top and input file and run the mdrun with -rerun option as described here. " http://manual.gromacs.org/online/mdp_opt.html#run";
Cheers, Rajesh On Thu, Jun 20, 2013 at 3:08 PM, Phan, Anh T. <[email protected]> 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Naga Rajesh Tummala, PhD Post-Doctoral Researcher, School of Chemistry and Biochemistry, Georgia Institute of Technology -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
