Hello Justin,<br><br>Thank you. I am using <br>gmxdump -s *.tpr -om to produce mdout.mdp file but I dont see box vector information. This error happens at the very beginning. I see no steps are calculated. <br><br><br><br>
<div class="gmail_quote">On 2 June 2011 13:11, 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 all,<br>
<br>
I am getting the error below at the very beginning of the simulation (both serial and parallel). I am sure I did not encounter this problem before with the same input files. This has just happened now. I really have no clue why this is happening. could you please help me? Thank you all in advance.<br>
<br>
<br>
Warning: Only triclinic boxes with the first vector parallel to 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>
</blockquote>
<br></div>
Your system is probably blowing up. "Nan" means "not a number," so the box vectors have become either infinitely large or small. Either the input coordinate file contained a malformed or non-existent box, or the simulation is collapsing along the way somewhere. Does the simulation run for a while before printing this, or is it right away?<br>
<br>
You can check the starting box vectors in the .tpr file with gmxdump to verify that they are sensible.<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;">
<br>
; Run control integrator = md dt = 0.002 nsteps = 1000000 ;5000 nstcomm = 100 <br><div class="im">
; Output control<br>
nstenergy = 100 nstxout = 100 nstvout = 0<br>
nstfout = 0<br>
nstlog = 1000 nstxtcout = 1000 <br>
; Neighbor searching<br>
nstlist = 10 ns_type = grid <br>
; Electrostatics/VdW<br>
coulombtype = Shift vdw-type = Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 <br>
; Cut-offs<br>
rlist = 1.25 rcoulomb = 1.0 rvdw = 1.0 <br>
; Temperature coupling Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 300 ; Pressure coupling<br>
Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 compressibility = 3.5e-5 ref_p = 10 <br>
; Velocity generation gen_vel = yes gen_temp = 300.0 gen_seed = 173529 <br>
; Bonds<br>
constraints = all-bonds constraint-algorithm = lincs<br>
<br>
<br>
</div></blockquote>
<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>
<br>
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