[gmx-users] Domain Decomposition

means? and what means 5065 and 16487? Regards, grita -- View this message in context: http://gromacs.5086.n6.nabble.com/Domain-Decomposition-tp4681762p4681762.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Protein charge

Hi all, I've a simple question: Is there a tool with which you can charge a protein after a certain pH-value? Best regards, grita -- View this message in context: http://gromacs.5086.n6.nabble.com/Protein-charge-tp4704321p4704321.html Sent from the GROMACS Users Forum mailing list archi

[gmx-users] what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

Hi, can someone tell me exactly what the \sigma in the LJ-potential in Gromacs is? Is \sigma the radius of a sphere or the diameter of a sphere? I am not so sure, because I want to calculate the parameters c^6 = 4 \epsilon \sigma^6 c^12 = 4 \epsilon \sigma^12. Best, grita -- View this

[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

oms? Best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/what-is-sigma-in-gromacs-the-radius-of-a-sphere-or-the-diameter-of-a-sphere-tp5010517p5010519.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@g

[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

Hi Justin, thanks for your help. What I want to understand is the following: I have two particles and the interaction diameter should be 5 angstroms. The \sigma in this formulas c^6 = 4 \epsilon \sigma^6 c^12 = 4 \epsilon \sigma^12 would be 5, or? Best, grita -- View this message in

[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

in the following formulas > c^6 = 4 \epsilon \sigma^6 > c^12 = 4 \epsilon \sigma^12 Is it so? Best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/what-is-sigma-in-gromacs-the-radius-of-a-sphere-or-the-diameter-of-a-sphere-tp5010517p5010523.html Sent from the G

[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

27;ve asked for this, because in other force fields there are different definitions of sigma. Sorry for the confusion. In short, the sigma is the separation or the 'diameter'. True or False ??? Best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/what-is-si

[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

Dear Richard, many thanks for this clarification. Best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/what-is-sigma-in-gromacs-the-radius-of-a-sphere-or-the-diameter-of-a-sphere-tp5010517p5010580.html Sent from the GROMACS Users Forum mailing list archive at

[gmx-users] GPU version of Gromacs

Hey guys, Is it possible to make a SD simulation with using the pull code in the GPU version of Gromacs? Best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/GPU-version-of-Gromacs-tp5010581.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com

[gmx-users] Re: GPU version of Gromacs

omputer with a CUDA graphic card. Many thanks, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/GPU-version-of-Gromacs-tp5010581p5010627.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http:

[gmx-users] Re: GPU version of Gromacs

Hi, Is it possible to calc the PME on the CUDA card? If it is possible, how can one do it? Best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/GPU-version-of-Gromacs-tp5010581p5010758.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com

[gmx-users] Several questions about the GPU version

. It would be very nice if someone or some people could answer the questions. Many thanks and best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/Several-questions-about-the-GPU-version-tp5010934.html Sent from the GROMACS Users Forum mailing list archive at Nabbl

[gmx-users] Preprocessor statements

Hi guys, Is it possible to specify in the topol.top file preprocessor statements, so that you can stop the simulation prematurely? I pull two molecules together and I'd like to stop the simulation if the center of mass distance of the molecules is less than xx nm. Best, grita -- View