Hi .. Can anybody tell me about *nrdf* (*radial distribution functions*) value that is in log file ..... How it effect our system !! Any link that I can follow to understand its role more clearly !!!
Thanks and Regards Lovika On Wed, Jun 17, 2015 at 10:54 AM, Lovika Moudgil <lovikamoud...@gmail.com> wrote: > Thanks Justin ..... Your suggestions helped me a lot .... I got it !!!! . > > > Regards > Lovika > > On Sun, Jun 7, 2015 at 7:23 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 6/6/15 2:03 AM, Lovika Moudgil wrote: >> >>> Hi Justin ... Thanks for being so supportive . I tried things as you said >>> and figured out that my slab is having problem with water . I have one >>> more question ... As I am working with golp ff parameters .. and it's >>> parameters are fine for water . Like if I put one water molecule on my >>> slab >>> ..and run my system ...Its doing well ...but if I do same things with box >>> full of water ... its not working !!! Is this possible?? Could it be >>> because of parameters compatibility Or could be because of my slab ???? >>> >>> >> Could be either. Maybe the definition of the water-slab parameters is >> wrong, such that one water only infrequently interacts and the crash is >> rare, whereas with a full box, the bad interaction comes up frequently. >> But at least it sounds like you've identified the problem. Now the issue >> is how to properly implement the GOLP parameters; if you did this yourself, >> check your work carefully. If you got the parameters from somewhere else, >> ask the person who created the files. >> >> -Justin >> >> >> >>> Thanks and Regards >>> Lovika >>> >>> On Fri, Jun 5, 2015 at 10:28 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> >>>> On 6/5/15 8:09 AM, Lovika Moudgil wrote: >>>> >>>> Hi Justin... Yes I agree my system is behaving absurdly . But I am >>>>> wondering why !!I have done minimization without any error ..here is >>>>> the >>>>> result ... >>>>> Steepest Descents converged to Fmax < 1000 in 1004 steps >>>>> Potential Energy = -9.6667906e+05 >>>>> Maximum force = 9.7920349e+02 on atom 796 >>>>> Norm of force = 1.7943926e+01 >>>>> ... I have One gold slab ...with golp parameters ..and amino acid on it >>>>> ...in box with water and Na , Cl ions ....Freezing is for gold >>>>> only.... >>>>> >>>>> >>>> So simplify the system - remove the gold layer and see if the remainder >>>> works, do a system of water + gold, etc. Your system is more complex >>>> than >>>> you're likely giving it credit for. Break it down - be scientific! >>>> >>>> System is not that big . And thing is temperature remain at the value >>>> >>>>> (that >>>>> is 300K) for few time after some time it start behaving weird . If >>>>> system >>>>> is wrong why its working even for one step ?? >>>>> >>>>> >>>>> Probably because the starting configuration is fine, but the >>>> trajectory >>>> evolves in such a way that it produces unreasonable physics. Freezing >>>> is a >>>> pretty severe perturbation. Investigate the validity of the force >>>> field. >>>> >>>> -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. >>>> >>>> >> -- >> ================================================== >> >> 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? 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