[gmx-users] Re: Re: Re: [gmx-usersCreating .top, .gro, .ndx, .itp files for TIP5Pwater

QUESTION WITHDRAWN QUESTION WITHDRAWN ***88 I think, I must use the command editconf *.gro bt dodecahedron d 0.5 o *.gro to generate the box of desired length. I didn't notice this command, hence was the confusion. Sorry for the disturbance and I

Re: Re: [gmx-users] Creating .top, .gro, .ndx, .itp files for TIP5Pwater

Thanks David for the reply. I was able to build topology file from the info given in the top directory. In contrast to the .gro file for TIP5P box, containing 516 water molecules, given at the top directory, I need a specific box size with exact number of water molecules (2

Re: [gmx-users] interaction energy of bulk TIP3P

> Hi All > > I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and PME > for 400 ps and extracted the interaction energy of a randomly picked water > molecule with rest of the system. > Simulation was done at 298K and 1bar and usual procedure for generating a > water box and equil

Re: [gmx-users] make hole question

3.1.4 or previous - Original Message - From: "Andrei Neamtu" <[EMAIL PROTECTED]> To: Sent: Saturday, November 17, 2007 11:29 PM Subject: [gmx-users] make hole question Hello gmx, I have a quick question: with what distribution of gromacs the mdrun make hole works? Cu bine, Andrei

[gmx-users] make hole question

Hello gmx, I have a quick question: with what distribution of gromacs the mdrun make hole works? Cu bine, Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://w

[gmx-users] interaction energy of bulk TIP3P

Hi All I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and PME for 400 ps and extracted the interaction energy of a randomly picked water molecule with rest of the system. Simulation was done at 298K and 1bar and usual procedure for generating a water box and equilibration were