Re: [gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg
On 2/9/15 11:00 AM, Agnivo Gosai wrote: Hi Antara Did you check the plot of the potential energy against the simulation time ? You can visualize the convergence of your energy minimisation from the above plot. Energy minimization, by definition, converges to some value (but there is no time in EM, it's not a dynamical process). That converged result is what is printed. There's usually nothing informative when EM converges without complaint. -Justin Thanks Regards Agnivo Gosai Grad Student, Iowa State University. On 2/9/15 7:41 AM, Antara mazumdar wrote: i got the following result after EM of this system of mine. writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 15280 steps Potential Energy = -5.0853170e+06 Maximum force = 9.9438867e+02 on atom 179440 Norm of force = 7.8095098e+00 Should i go ahead with NVT and NPT? -- Is there a reason you think you shouldn't? What outcome do you expect? Does this outcome meet that expectation? Does the structure look sensible? -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] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg
On 2/9/15 7:41 AM, Antara mazumdar wrote: i got the following result after EM of this system of mine. writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 15280 steps Potential Energy = -5.0853170e+06 Maximum force = 9.9438867e+02 on atom 179440 Norm of force = 7.8095098e+00 Should i go ahead with NVT and NPT? -- Is there a reason you think you shouldn't? What outcome do you expect? Does this outcome meet that expectation? Does the structure look sensible? -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.
[gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg
i got the following result after EM of this system of mine. writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 15280 steps Potential Energy = -5.0853170e+06 Maximum force = 9.9438867e+02 on atom 179440 Norm of force = 7.8095098e+00 Should i go ahead with NVT and NPT? -- Regards, Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- 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.
