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
