[gmx-users] lost ngmx

Hello gmx-users I have compiled gromacs on Debian/Linux wiht the option --with-x but the ngmx binary has not been generated. I don´t have gnome or kde installed, but I have installed xserver-xorg and I can export VMD with ssh. Do I need to install gnome or kde? if the answer is yes, Do I need

Re: [gmx-users] >60% slowdown with GPU / verlet and sd integrator

The paper looks good. Do some more work and publish many Sent from my iPhone On 17-Jan-2013, at 8:18 PM, "James Starlight" wrote: Dear Gromacs Developers! Using sd1 integrator I've obtain good performance with the core-5 + GTX 670 ( 13ns\per day) for the system of 60k atoms. That results on

RE: [gmx-users] Test mail

ok Date: Sat, 17 Dec 2011 16:33:25 +0530 From: priya.thiyagaraja...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Test mail Greetings, THis is a mail to test my gromacs mailing list connection -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listi

[gmx-users] problem in running grompp

Hello, when I run grompp I get the following error message always. Whoever has a correct fix to get rid of this error message and get the actual result, Please suggest. Thanking you Dr. Victor A. Doss _ The new Windows

[gmx-users] problem running grompp - error message here

Hello, when I run grompp I get the following error message always. Whoever has a correct fix to get rid of this error message and get the actual result, Please suggest. Thanking you Dr. Victor A. Doss processing topology... Generated 332520 of the 332520 non-bonded parameter combinations

[gmx-users] residual negative charge?

ametrizing? Thanx Victor M. Rosas García Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypa

[gmx-users] box of water with ions

topology files I saw in the gromacs documentation. Needless to say, I am FAR from being an experienced gromacs user, although I do have experience in computational chemistry, just not molecular dynamics. Any recommendations? Victor M. Rosas García, PhD Coordinador del Posgrado en Ciencias

[gmx-users] polarizable water?

Hello everybody, Currently, I have a SPC water box with some Ca(2+) and CO3(2-) ions swimming around (I defined the itp file for carbonate, got the charges from ab initio calcs, the whole system is electroneutral). How do I define the water to be polarizable? Regards Victor M. Rosas García