Re: [gmx-users] error: Only triclinic boxes...

[Justin A. Lemkul]

Elisabeth wrote:
Dear Justin,

I find:


box (3x3):
   box[    0]={ 1.60000e+01,  0.00000e+00,  0.00000e+00}
   box[    1]={ 0.00000e+00,  1.60000e+01,  0.00000e+00}
   box[    2]={ 0.00000e+00,  0.00000e+00,  1.60000e+01}
box_rel (3x3):
   box_rel[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   box_rel[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
   box_rel[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
boxv (3x3):
   boxv[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   boxv[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   boxv[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
pres_prev (3x3):
   pres_prev[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   pres_prev[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   pres_prev[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
svir_prev (3x3):
   svir_prev[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   svir_prev[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   svir_prev[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
fvir_prev (3x3):
   fvir_prev[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fvir_prev[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fvir_prev[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
nosehoover_xi: not available
x (2896x3):
   x[    0]={-7.49400e+00,  4.57000e-01,  5.00000e-01}
   x[    1]={-7.58200e+00,  5.21000e-01,  5.00000e-01}
   x[    2]={-7.49600e+00,  3.94000e-01,  4.11000e-01}
   x[    3]={-7.49600e+00,  3.94000e-01,  5.89000e-01}
   x[    4]={-7.36800e+00,  5.43000e-01,  5.00000e-01}
   x[    5]={-7.36800e+00,  6.06000e-01,  5.89000e-01}
   x[    6]={-7.36800e+00,  6.06000e-01,  4.11000e-01}
   x[    7]={-7.24200e+00,  4.57000e-01,  5.00000e-01}
   x[    8]={-7.24200e+00,  3.94000e-01,  4.11000e-01}
   x[    9]={-7.24200e+00,  3.94000e-01,  5.89000e-01}
   x[   10]={-7.11700e+00,  5.43000e-01,  5.00000e-01}
   x[   11]={-7.11700e+00,  6.06000e-01,  5.89000e-01}
   x[   12]={-7.11700e+00,  6.06000e-01,  4.11000e-01}
   x[   13]={-6.99100e+00,  4.57000e-01,  5.00000e-01}

I made box bigger to remove bad contacts in initial configuration 
(although I have been using the same gro file before and never got such 
error). Do you recommend I reinstall 4.5.4 ?


Simply increasing a box size may not alleviate bad contacts in and of itself. 
Plus, you're applying high pressure (10 bar), which is probably just causing the 
box to rapidly collapse in on itself due to void space.

I doubt reinstalling would do any good.  If your installation was severely 
broken, nothing would be working.

-Justin

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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