Re: [gmx-users] How to center one - solute in the water box?

Chih-Ying Lin wrote: Hi the command editconf -center 0, 0 , 0 This command will make the water system center (0,0,0). How to put one-solute in the center of the water box? From editconf -h: -[no]c bool no Center molecule in box (implied by -box and -d) -Justin Thank you

[gmx-users] How to center one - solute in the water box?

Hi the command editconf -center 0, 0 , 0 This command will make the water system center (0,0,0). How to put one-solute in the center of the water box? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/l

Re: [gmx-users] editconf -density 1000

Chih-Ying Lin wrote: Hi The flag of editconf -density has the default value 1000 editconf -densityreal1000Density (g/l) of the output box achieved by scaling But, my system is running on D2O not H2O Earlier I did not notice this flag and simply use the command editconf to crea

[gmx-users] editconf -density 1000

Hi The flag of editconf -density has the default value 1000 editconf -densityreal1000Density (g/l) of the output box achieved by scaling But, my system is running on D2O not H2O Earlier I did not notice this flag and simply use the command editconf to create a box. So, will my sim

Re: [gmx-users] the solute out of water box

Chih-Ying Lin wrote: Hi What does it mean "the solute running out of water box" ? What tool is reporting this message? Did it mean that my simulation fail? I would suggest reading about periodic boundary conditions. Furthermore, check the list archive before posting. If you search "pro

[gmx-users] the solute out of water box

Hi What does it mean "the solute running out of water box" ? Did it mean that my simulation fail? How to fix this problem? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] distance restraints and domain decomposition

Hi All, I am trying to run a simulation on a 13 residue peptide fragment with distance restraints in parallel and I'm getting a fatal error when I try to implement mdrun. Here is my nohup.out file: :-) G R O M A C S (-: Giving Russians Opium May Al

[gmx-users] parallel run

Hello I want to know suitable speed of network for parallel run I heard 1Giagabit Network is not enough and I havnt good performance at 1Gigabit , thank you ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/list

[gmx-users] Two questions about virial calculation

Hi all I looked into the file named bondfree.c of Gromacs-4.0 for bond, angle and dihedral force contribution to the virial. And I have one problem that I can't understand. When the periodicity has been taken into account for the virial why do you put one atom's contribution to virial in the c

Re: [gmx-users] crash on Source code file: nsgrid.c, line: 226

Egidijus Kuprusevicius wrote: Dear developers, I have got this message on the crash (system with 192 molecules, paralellipiped) Search the list archives, there are hundreds of posts related to this error (mdrun even gave you some tips). For general reference: http://wiki.gromacs.org/in

[gmx-users] crash on Source code file: nsgrid.c, line: 226

Dear developers, I have got this message on the crash (system with 192 molecules, paralellipiped)   --- Program mdrunmpi, VERSION 3.3 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each

RE: [gmx-users] g_bundle: How are these three terms defined? - (1) Tilt (2) Tiltr, and (3) Tiltl

Hi, The description describes this very concisely. Tilt is the angle between the axis vector with the reference vector. Tiltr is the radial tilt, so the angle between the reference vector with the projection of the axis vector on the plane through the reference vector and the midpoint of the axis

Re: [gmx-users] how to set up a rigid system

To set up rigid system, you need to put (3n-6) constraints (in the form of bond, angle), where n is the atom/bead (in the case of coarse-grain model) number in the molecule. YY On Fri, Dec 5, 2008 at 1:03 PM, Xin Liu <[EMAIL PROTECTED]> wrote: > Dear GMX users, > > > I am carrying out MD simulat