Re: [gmx-users] RDF plot with large g(r) values
makes sense now, your system is quite heterogeneous. you may use your RDF but some reviewers might not agree with this kind of analysis for heterogeneous systems, so you have to explain why your correlation peaks are so high and why the profiles don't converge to unity. On Fri, Jan 9, 2015 at 12:34 AM, Kester Wong kester2...@ibs.re.kr wrote: Hi Andre, Thank you for your input. *보낸사람* : André Farias de Moura mo...@ufscar.br *받는사람* : Discussion list for GROMACS us gmx-us...@gromacs.org *받은날짜* : 2015년 1월 8일(목) 22:05:39 *제목* : Re: [gmx-users] RDF plot with large g(r) values RDF values are sensitive to the volume of the system, so if you put the same solutes inside a larger/smaller box, RDF values change accordingly (check basic definitions of RDF in simulation handbooks to make sure you understand this relation). Ah right, that explains why my RDF values dropped if I put a larger amount of water in the same box. and even if you have the same size and composition, RDF may become really large if molecules aggregate. Yep, I have a droplet where the Na+ and OH- ions tend to aggregate within the solution, the high g(r) peak in the RDF almost doubles the other systems with no aggregation. In this case, can I still use my RDF plots? Regards, Kester On Thu, Jan 8, 2015 at 7:48 AM, Kester Wong wrote: Dear all, My apologies if this question sounds too basic of if it has been covered. I did some RDF calculations, and as when I plotted the figures, the g(r) values are in the hundreds, whereas the papers that I have seen are all in the range of 0-12. The x-axis (nm), however, seemed to be correct. Regards, Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF plot with large g(r) values
Hi Andre,Thank you for your input.보낸사람 : "André Farias de Moura" mo...@ufscar.br받는사람 : Discussion list for GROMACS us gmx-us...@gromacs.org받은날짜 : 2015년 1월 8일(목) 22:05:39제목 : Re: [gmx-users] RDF plot with large g(r) valuesRDF values are sensitive to the volume of the system, so if you put the same solutes inside a larger/smaller box, RDF values change accordingly (check basic definitions of RDF in simulation handbooks to make sure you understand this relation).Ah right, that explains why my RDF values dropped if I put a larger amount of water in the same box. and even if you have the same size and composition, RDF may become really large if molecules aggregate.Yep, I have a droplet where the Na+ and OH- ions tend to aggregate within the solution, the high g(r) peak in the RDF almost doubles the other systems with no aggregation.In this case, can I still use my RDF plots?Regards,Kester On Thu, Jan 8, 2015 at 7:48 AM, Kester Wong <kester2...@ibs.re.kr> wrote: Dear all, My apologies if this question sounds too basic of if it has been covered. I did some RDF calculations, and as when I plotted the figures, the g(r) values are in the hundreds, whereas the papers that I have seen are all in the range of 0-12. The x-axis (nm), however, seemed to be correct. Regards, Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF plot with large g(r) values
Dear Justin, No, I am not comparing equivalent systems, nor reproducing previous findings. My simulation box contains a droplet of 2000 water molecules on graphene.The RDF of g(r) Ow-Ow shows a first peak at r = 0.3 nm, with a peak height of 400.For 6000 and 10,000 water molecules, the peak heights are 200 and 100, respectively. Is this due to the large vacuum in my simulation box?Regards,KesterOn 1/8/15 4:48 AM, Kester Wong wrote: Dear all, My apologies if this question sounds too basic of if it has been covered. I did some RDF calculations, and as when I plotted the figures, the g(r) values are in the hundreds, whereas the papers that I have seen are all in the range of 0-12. Are you comparing equivalent systems, e.g. trying to reproduce previous findings? If not, it's just apples and oranges. Your result is not necessarily unusual. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF plot with large g(r) values
On 1/8/15 4:48 AM, Kester Wong wrote: Dear all, My apologies if this question sounds too basic of if it has been covered. I did some RDF calculations, and as when I plotted the figures, the g(r) values are in the hundreds, whereas the papers that I have seen are all in the range of 0-12. Are you comparing equivalent systems, e.g. trying to reproduce previous findings? If not, it's just apples and oranges. Your result is not necessarily unusual. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF plot with large g(r) values
RDF values are sensitive to the volume of the system, so if you put the same solutes inside a larger/smaller box, RDF values change accordingly (check basic definitions of RDF in simulation handbooks to make sure you understand this relation). and even if you have the same size and composition, RDF may become really large if molecules aggregate. On Thu, Jan 8, 2015 at 7:48 AM, Kester Wong kester2...@ibs.re.kr wrote: Dear all, My apologies if this question sounds too basic of if it has been covered. I did some RDF calculations, and as when I plotted the figures, the g(r) values are in the hundreds, whereas the papers that I have seen are all in the range of 0-12. The x-axis (nm), however, seemed to be correct. Regards, Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
