[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
Re: [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?
On 15 Aug 2013 15:27, grita cemilyi...@arcor.de wrote In short, the sigma is the separation or the 'diameter'. True or False ??? Neither. The diameter of a particle is a meaningless concept here. You have a continuous potential, not a definite boundary. If you want your particles to *almost* never come closer than a certain distance, you need the potential to be positive and much higher than the average thermal energy at that distance. How to translate this in numbers depends on your specific needs. -- 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 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
Re: [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?
On 8/15/13 8:28 AM, grita wrote: 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? No. There are no explicit settings for particle size anywhere in Gromacs (with the possible exception of vdwradii.dat, but that's only used by genbox and g_sas). Dynamics rely on inter-particle potentials. You would have to derive and/or tune parameters that represent physical reality of what a particle's size should be such that it is reflected in the outcome of MD. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
Re: [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?
You have to define what do you mean by interaction diameter. 2013/8/15 grita cemilyi...@arcor.de 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 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
Re: [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?
On 8/15/13 8:58 AM, grita wrote: 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? It's still not entirely clear. Is the value of the LJ potential zero when the two spheres are at a 5-A separation? If it is, then that's the value of sigma. If the 5-A separation defines the energy minimum for the interaction between the two particles, then that's not sigma, the 5 A value would be r_m, from which sigma can be calculated. None of this guarantees that the spheres will not overlap, given the form of the LJ potential. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
Re: [gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?
Dear Grita, \sigma in gromacs is the value of \sigma in a Lennard-Jones (LJ) potential defined by: 4\epsilon*[(sigma/r)^12-(sigma/r)^6], where r is the separation between the two point particles, epsilon is the well depth, and \sigma is a length scale which characterises the interaction between two particles. This is the same as in the wikipedia article Justin linked to or numerous other websites, journal articles, and text books discussing the LJ potential. The particles if they have sufficient energy can move closer than \sigma together or they can move further apart than \sigma. As Justin said there is no such thing as a particles diameter in gromacs everything is a point particle with no radius or diameter. If you want something where the particles absolutely cannot overlap regardless of their energy you will need to consider hard-sphere potentials. However, as these are not continuous and therefore not really suited to MD simulations I doubt that's what you want. Richard On 15/08/13 14:26, grita wrote: 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
