Dear Justin,<br><br>I find:<br><br><br>box (3x3):<br> box[ 0]={ 1.60000e+01, 0.00000e+00, 0.00000e+00}<br> box[ 1]={ 0.00000e+00, 1.60000e+01, 0.00000e+00}<br> box[ 2]={ 0.00000e+00, 0.00000e+00, 1.60000e+01}<br>
box_rel (3x3):<br> box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> box_rel[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}<br> box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}<br>boxv (3x3):<br>
boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>pres_prev (3x3):<br> pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>svir_prev (3x3):<br> svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>fvir_prev (3x3):<br> fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
nosehoover_xi: not available<br>x (2896x3):<br> x[ 0]={-7.49400e+00, 4.57000e-01, 5.00000e-01}<br> x[ 1]={-7.58200e+00, 5.21000e-01, 5.00000e-01}<br> x[ 2]={-7.49600e+00, 3.94000e-01, 4.11000e-01}<br>
x[ 3]={-7.49600e+00, 3.94000e-01, 5.89000e-01}<br> x[ 4]={-7.36800e+00, 5.43000e-01, 5.00000e-01}<br> x[ 5]={-7.36800e+00, 6.06000e-01, 5.89000e-01}<br> x[ 6]={-7.36800e+00, 6.06000e-01, 4.11000e-01}<br>
x[ 7]={-7.24200e+00, 4.57000e-01, 5.00000e-01}<br> x[ 8]={-7.24200e+00, 3.94000e-01, 4.11000e-01}<br> x[ 9]={-7.24200e+00, 3.94000e-01, 5.89000e-01}<br> x[ 10]={-7.11700e+00, 5.43000e-01, 5.00000e-01}<br>
x[ 11]={-7.11700e+00, 6.06000e-01, 5.89000e-01}<br> x[ 12]={-7.11700e+00, 6.06000e-01, 4.11000e-01}<br> x[ 13]={-6.99100e+00, 4.57000e-01, 5.00000e-01}<br><br>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 ?<br>
<br>Appreciate any help...<br><br>Regards,<br><br> <br><br><div class="gmail_quote">On 2 June 2011 14:47, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
Elisabeth wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello Justin,<br>
<br>
Thank you. I am using<br>
gmxdump -s *.tpr -om to produce mdout.mdp file but I dont see box <br>
</blockquote>
<br></div>
You don't need an mdout.mdp file, nor would box vectors be present in one. What you're looking for is the box information present in the .tpr file. Run:<br>
<br>
gmxdump -s topol.tpr > out<br>
<br>
Then search in the "out" file for the box information.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
vector information. This error happens at the very beginning. I see no steps are calculated.<br>
<br>
</blockquote>
<br></div>
Then the input box information is likely corrupt, or the simulation blows up at the very start of the simulation (i.e. step 0).<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
<br>
<br>
On 2 June 2011 13:11, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Elisabeth wrote:<br>
<br>
Hello all,<br>
<br>
I am getting the error below at the very beginning of the<br>
simulation (both serial and parallel). I am sure I did not<br>
encounter this problem before with the same input files. This<br>
has just happened now. I really have no clue why this is<br>
happening. could you please help me? Thank you all in advance.<br>
<br>
<br>
Warning: Only triclinic boxes with the first vector parallel to<br>
the x-axis and the second vector in the xy-plane are supported.<br>
Box (3x3):<br>
Box[ 0]={ nan, 0.00000e+00, 0.00000e+00}<br>
Box[ 1]={ nan, nan, nan}<br>
Box[ 2]={ nan, nan, nan}<br>
Can not fix pbc.<br>
<br>
<br>
Your system is probably blowing up. "Nan" means "not a number," so<br>
the box vectors have become either infinitely large or small.<br>
Either the input coordinate file contained a malformed or<br>
non-existent box, or the simulation is collapsing along the way<br>
somewhere. Does the simulation run for a while before printing<br>
this, or is it right away?<br>
<br>
You can check the starting box vectors in the .tpr file with gmxdump<br>
to verify that they are sensible.<br>
<br>
-Justin<br>
<br>
<br>
; Run control integrator = md dt = 0.002 nsteps = 1000000 ;5000 nstcomm = 100 ; Output control<br>
nstenergy = 100 nstxout =<br>
100 nstvout = 0<br>
nstfout = 0<br>
nstlog = 1000 nstxtcout = 1000<br>
; Neighbor searching<br>
nstlist = 10 ns_type =<br>
grid ; Electrostatics/VdW<br>
coulombtype = Shift vdw-type = Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ; Cut-offs<br>
rlist = 1.25 rcoulomb = 1.0 rvdw = 1.0 ; Temperature coupling Tcoupl = v-rescale<br>
tc-grps = System tau_t<br>
= 0.1 ref_t = 300 ; Pressure coupling<br>
Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 compressibility = 3.5e-5 ref_p = 10 ; Velocity generation gen_vel =<br>
yes gen_temp = 300.0 gen_seed = 173529 ; Bonds<br>
constraints = all-bonds constraint-algorithm = lincs<br>
<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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