@Justin, actually. After a second thought and closer examination in VMD using RESTYPE differentiation, maybe this is the correct output because 95% of the beads shown are hydrophobic so they probably like to clump together after 100000 time step …. I'm going to shorten my nstep in MD and see if I get a less clumped structure.
Thank you Justin, and sorry for the impulsive question. I'll let you know if there is a further problem. Thanks, Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering [email protected] On Jan 5, 2013, at 8:45 PM, Xu Dong Huang <[email protected]> wrote: > for some reason my message is too long and held for approval, but anyway, > Starting Energy Minimized structure: > http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2013-01-05at83539PM_zpsc12357ca.png > > Ending NVT outcome .gro structure: > http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2013-01-05at83509PM_zpsb4f658b2.png > > @Justin, this is the same star polymer you've seen before, and I assume you > were aware that there is a definite bond interaction definition and etc. (So > I don't think the structure should have blown up like that) > > MDP information: > integrator = md > tinit = 0.0 > dt = 0.02 > nsteps = 100000 > nstcomm = 1 > comm-grps = > > nstxout = 100 > nstvout = 100 > nstfout = 0 > nstlog = 100 > nstenergy = 100 > nstxtcout = 0 > xtc_precision = 1000 > xtc-grps = > energygrps = system > > nstlist = 10 > ns_type = grid > pbc = xyz > rlist = 1.4 > coulombtype = Shift > rcoulomb_switch = 0.0 > rcoulomb = 1.2 > epsilon_r = 15 > vdw_type = Shift > rvdw_switch = 0.9 > rvdw = 1.2 > DispCorr = No > tcoupl = V-rescale > tc-grps = system > tau_t = 1.0 > ref_t = 300 > Pcoupl = no > Pcoupltype = isotropic > tau_p = 1.0 > compressibility = 3e-4 > ref_p = 1.0 > gen_vel = yes > gen_temp = 300 > gen_seed = 473529 > constraints = none > constraint_algorithm = Lincs > unconstrained_start = no > lincs_order = 4 > lincs_warnangle = 30 > > The topology is the same one from last time I sent you, a star. bond order > defined. (Can't attach it on here because it's too long and my message will > be held for approval by gmx) > > Xu Dong Huang > Chemical & Biochemical Engineering > Rutgers School of Engineering > [email protected] > > On Jan 5, 2013, at 8:31 PM, Justin Lemkul <[email protected]> wrote: > >> >> >> On 1/5/13 8:29 PM, Xu Dong Huang wrote: >>> Dear users, >>> >>> I have a defined polymer .gro file and I ran energy minimization on it. >>> However, when I attempt to run NVT on the polymer in a vacuum (box, no >>> solvent), and I view the output .gro and trajectory in VMD, I see that my >>> polymer is no longer a star, the beads are flying in every random >>> direction, no beads are in bond connection as they should be. Any insight >>> into why my polymer blew up in vacuum? (please let me know what kind of >>> additional information you'd like to see) >>> >> >> At minimum, you need to post the contents of your topology and .mdp file. >> Without that information, no one can make any assessment of what's going on. >> Images of the starting and ending configurations can also be useful. >> >> -Justin >> >> -- >> ======================================== >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
