@Justin, Yeah I allowed the NVT to run for way too long. Therefore I get a super clumped structure. (Where as I only wanted a slightly clumped structure). I reduced the nsteps to about 3000 from 100 thousand to achieve my desired structure.
Thanks for the support. Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 5, 2013, at 8:51 PM, Xu Dong Huang <xudo...@eden.rutgers.edu> wrote: > @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 > xudo...@eden.rutgers.edu > > On Jan 5, 2013, at 8:45 PM, Xu Dong Huang <xudo...@eden.rutgers.edu> 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 >> xudo...@eden.rutgers.edu >> >> On Jan 5, 2013, at 8:31 PM, Justin Lemkul <jalem...@vt.edu> 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 gmx-users@gromacs.org >>> 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. 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