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

[Xu Dong Huang]

@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 
xudongh at eden.rutgers.edu 

On Jan 5, 2013, at 8:45 PM, Xu Dong Huang <xudongh at 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 
> xudongh at eden.rutgers.edu 
> 
> On Jan 5, 2013, at 8:31 PM, Justin Lemkul <jalemkul at 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
>> 
>> ========================================
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