[gmx-users] solvent except water

2010-01-16 Thread leila karami
Hi what command and what option apply solvent except water in MD simulation by gromacs. Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

Re: [gmx-users] solvent except water

2010-01-16 Thread David van der Spoel
leila karami wrote: Hi what command and what option apply solvent except water in MD simulation by gromacs. Any help will highly appreciated! WHat do you mean? -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University.

[gmx-users] solvent except water

2010-01-16 Thread leila karami
Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

Re: [gmx-users] solvent except water

2010-01-16 Thread David van der Spoel
leila karami wrote: Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami OK, now I understand. You can give to genbox any solvent that you like, provided that each molecule consists of a single residue (the residue

Re: [gmx-users] solvent except water

2010-01-16 Thread rasoul nasiri
Hi I want to use a solvent with two types molecules (for example linear and cyclic Glucose form). How can I fill box with them? I highly appreciate for advice given me! Best Regards Rasoul On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: leila karami wrote:

Re: [gmx-users] solvent except water

2010-01-16 Thread David van der Spoel
rasoul nasiri wrote: Hi I want to use a solvent with two types molecules (for example linear and cyclic Glucose form). How can I fill box with them? You can use genbox with mixed solvents. I highly appreciate for advice given me! Best Regards Rasoul On Sat, Jan 16, 2010 at 11:42 AM,

Re: [gmx-users] solvent except water

2010-01-16 Thread Justin A. Lemkul
David van der Spoel wrote: rasoul nasiri wrote: Hi I want to use a solvent with two types molecules (for example linear and cyclic Glucose form). How can I fill box with them? You can use genbox with mixed solvents. There are even how-to's on the Gromacs site to accomplish this:

[gmx-users] Scaling of Coordinates is Occurring - why?

2010-01-16 Thread chris . neale
From what I can find, it seems that you are correct to assume that frozen coordinates should not be scaled: http://lists.gromacs.org/pipermail/gmx-users/2002-July/002054.html and, from the online manual: freezegrps: Groups that are to be frozen (i.e. their X, Y, and/or Z position

Re: [gmx-users] Scaling of Coordinates is Occurring - why?

2010-01-16 Thread David van der Spoel
chris.ne...@utoronto.ca wrote: From what I can find, it seems that you are correct to assume that frozen coordinates should not be scaled: http://lists.gromacs.org/pipermail/gmx-users/2002-July/002054.html and, from the online manual: freezegrps: Groups that are to be frozen (i.e. their

[gmx-users] Re: implicit wall doesn't recognize the wall_atomtype correctly?

2010-01-16 Thread Qiao Baofu
Hi, Firstly, regarding my last email, even though I didn't get any complain about the nonsense setting for the wall_atomtype from grompp, the mdrun is crashed after some steps. Then I tested some atomtypes which have been given in OPLS, and checked the output in md.log: a) When wall_atomtype =

[gmx-users] The size of the domain decomposition grid (1) does not match the number of nodes (8).

2010-01-16 Thread chris . neale
Hello, I have a run that was working fine under parallel mdrun -pd and when I then switched to domain decomposition I got: Fatal error: The size of the domain decomposition grid (1) does not match the number of nodes (8). The total number of nodes is 8 while running like this: