@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 & Bioc
@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 10
time step …. I'm going to shorten my nstep in MD and see i
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
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/Scre
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
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
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