[gmx-users] Domain Decomposition
Hi, I'm trying to run a CG SD simulation, but I get this: Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: LJ-14 of 5065 missing 1 exclusions of 16487 missing 1 What does it 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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 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-tp5010517.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?
Hi Justin, Wikipedia says: "sigma is the finite distance at which the inter-particle potential is zero" But if I want to simulate particles with a certain diameter, where can I set the diameter in Gromcas?. For example, a sphere with a diameter of 5 angstroms, would then sigma 5 angstroms? 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@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 context: http://gromacs.5086.x6.nabble.com/what-is-sigma-in-gromacs-the-radius-of-a-sphere-or-the-diameter-of-a-sphere-tp5010517p5010521.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?
Hi, with "interaction diameter" I mean the following: I have two spheres with a radii of 2.5 angstrom. The spheres should not overlap. >From that, I derive my 'interaction diameter'/'interaction distance' 5 angstrom. Now, the 5 angstroms should be the \sigma 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 GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?
Hi Justin, yes, the LJ potential is zero when the two spheres are at a separation of 5 angstrom. So, I can be sure, that in this case the \sigma in c^6 = 4 \epsilon \sigma^6 c^12 = 4 \epsilon \sigma^12 are the seperation or 'my interaction diameter / interaction distance'??? I'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-sigma-in-gromacs-the-radius-of-a-sphere-or-the-diameter-of-a-sphere-tp5010517p5010526.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: GPU version of Gromacs
Dear Dwey & Justin, I've not tried it yet and I've asked because in the 4.5.x GPU version of Gromacs not all features were supported. In my simulations I'm using the SD integrator and the Pull-Code. Since both are supported in the current GPU version, I will try it on a computer 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Several questions about the GPU version
Hey guys, Meanwhile I run my simulations on a CUDA card and must say that I am very very satisfied with it. Nevertheless I have a few questions regarding to a improved performance: 1. Is it possible to perform the PME calculation on the CUDA card? I always see in md.log that the PME runs on the CPU, even if the flag -nb gpu is set. 2. Is it possible to run multiple simulations on one CUDA card? If so, how and is there an engine program for the management (like on clusters)? 3. I don't understand the sense of the mdp option coulomb-modifier. What should it cause? I set it to none. 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 Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 this message in context: http://gromacs.5086.x6.nabble.com/Preprocessor-statements-tp5011469.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
