[gmx-users] more than 5 digits of the number of atoms and residue

Dear GROMACS users and developers, In the .gro files, there are only 5 digits reserved for the atom number and residue number. But if I have more than 1 million atoms or residues, may I just increase the column number from 5 to 6? I guess not, then how to simulate such system? Thanks, Cherry

[gmx-users] center of mass motion

Dear Gromacs users and developers, I am studying a system consisting of six molecules (3 groups). I would like to keep the center-of-mass motion of each molecule with the system having zero center-of-mass motion. So I set comm_mode=Linear. In the simulation, immediately the center-of-mass motion o

RE: [gmx-users] configuration error

26, 2006 9:10 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] configuration error Cherry Y. Yates wrote: > Dear gromacs developlers, > > When I tried to parallelize GROMACS with intel > fortran/C compiler on a Athlon cluster, I met this > kind of error: > > $

[gmx-users] configuration error

Dear gromacs developlers, When I tried to parallelize GROMACS with intel fortran/C compiler on a Athlon cluster, I met this kind of error: $ ./configure --enable-mpi . checking size of int... configure: error: cannot compute sizeof (int), 77 What is wrong? Needs help! Thanks, Cherry

[gmx-users] tersoff potential

Dear Developers, I wonder if the Tersoff potential is implemented in GROMACS. Many thanks, Cherry Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com

Re: [gmx-users] temperature shooting up

itial water geometry is not the same as the rigid model, does the program will "enforce" that geometry for water molecules, or to "relax" water molecure towards it? Many thanks,CherryMark Abraham <[EMAIL PROTECTED]> wrote: Cherry Y. Yates wrote:> Dear Mark,> &

[gmx-users] temperature shooting up

from 300K to thousands degree, the total energy is going up also instead of fluctuating. I attached both the itp files and grompp.mdp files. Let me know what could be wrong. It is really wired to me. Thanks,CherryMark Abraham <[EMAIL PROTECTED]> wrote: Cherry Y. Yates wrote:> Dear GROMACS d

[gmx-users] no temperature coupling

Dear GROMACS developers,I would like to do a SPC-water simulation without temperature coupling. I set tcouple to 300K and did Berenderson T-coupling first for 400 ps to equilibrate the system. Then I copy confout.gro to conf.gro, set tcoupl to no. However the Temperature of the later similation ju

[gmx-users] POL5/TZ polarizable water model .itp file

Dear Gromacs users and developers,I wonder if anyone has an itp file for the POL5/TZ polarizable water model (H. A. Stern, F. Rittner, B. J. Berneand R. A. Friesner, J. Chem. Phys. 115 (2001)2237-2251.). Thank you very much.Cherry Do you Yahoo!? Ev

Re: [gmx-users] periodic boundary condition

GMXLIB path variable)Could you tell me what is wrong? Many thanks!!!CherryDavid van der Spoel <[EMAIL PROTECTED]> wrote: Cherry Y. Yates wrote:> Dear gromacs developers and users,> > I am calculating a nanotube which has periodic boundary condition along > one direction. I wonder

[gmx-users] periodic boundary condition

Dear gromacs developers and users,I am calculating a nanotube which has periodic boundary condition along one direction. I wonder how to make an itp file for this system. The difficulty lies in describing the bond between two end atoms, e.g., two atoms are bonded in an infinite length system, but a

[gmx-users] how to exclude some atoms from coulomb interaction calculation?

Dear all,I did a massive MD simulation of nanostructure. In my calculation, over 80% atoms have zero charge and the main CPU time is devoted to Coulomb interaction. I wonder if anyone knows how to exclude these neutral atoms from Coublomb interaction so that a lot of CPU time will be saved.Many tha