[gmx-users] after NVT run, molecule becomes dispersed/ loose

[Justin Lemkul]

On 1/5/13 8:45 PM, Xu Dong Huang 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)
>

The topology is the most important bit of information.  Please post a link where 
it can be downloaded.  What are your box vectors?  What is the minimum 
box-solute distance?

-Justin

-- 
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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

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