hi Justin... you were right.. my equilibration is ýnsufficient...ý increase nsteps 50000....200000..now ý recieve this message..<br><br>Fatal error:<br>The Z-size of the box (1.957000) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (2) times the smallest allowed cell size (1.000000)<br>
<br>How can ý solve this problem...please help me...<br><br><div class="gmail_quote">1 Þubat 2012 22:37 tarihinde Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> yazdý:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im"><br>
<br>
mehmet kýytak wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
hi justin<br>
ý used this mdp. file ..simulation box may be wrong.?..ý used dodecahedron distance edge 2.0 nm.....<br>
<br>
</blockquote>
<br></div>
No, that's almost certainly not the problem. Insufficient minimization/equilibration, or instability due to the use of the free energy code is more likely. You look to be trying to decouple the entire system, which could be an unstable process. You haven't said what you're doing, so I won't hazard a guess at this point. Please refer to the link I provided and try running without the free energy code. Otherwise, you're (potentially) trying to solve several problems at once.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
; Run control<br>
integrator = sd ; Langevin dynamics<br>
tinit = 0<br>
dt = 0.002<br>
nsteps = 2500000 ; 5 ns<br>
nstcomm = 100<br>
; Output control<br>
nstxout = 0<br>
nstvout = 0<br>
nstfout = 0<br>
nstlog = 0<br>
nstenergy = 0<br>
nstxtcout = 0<br>
xtc-precision = 1000<br>
; Neighborsearching and short-range nonbonded interactions<br>
nstlist = 10<br>
ns_type = grid<br>
pbc = xyz<br>
rlist = 1.0<br>
; Electrostatics<br>
coulombtype = PME<br>
rcoulomb = 1.0<br>
; van der Waals<br>
vdw-type = switch<br>
rvdw-switch = 0.8<br>
rvdw = 0.9<br>
; Apply long range dispersion corrections for Energy and Pressure<br>
DispCorr = EnerPres<br>
; Spacing for the PME/PPPM FFT grid<br>
fourierspacing = 0.12<br>
; EWALD/PME/PPPM parameters<br>
pme_order = 6<br>
ewald_rtol = 1e-06<br>
epsilon_surface = 0<br>
optimize_fft = no<br>
; Temperature coupling<br>
; tcoupl is implicitly handled by the sd integrator<br>
tc_grps = system<br>
tau_t = 1.0<br>
ref_t = 300<br>
; Pressure coupling is on for NPT<br>
Pcoupl = Parrinello-Rahman<br>
tau_p = 0.5<br>
compressibility = 4.5e-05<br>
ref_p = 1.0<br>
; Free energy control stuff<br>
free_energy = yes<br>
init_lambda = 0.0<br>
delta_lambda = 0<br>
foreign_lambda = 0.05<br>
sc-alpha = 0.5<br>
sc-power = 1.0<br>
sc-sigma = 0.3<br>
couple-moltype = system ; name of moleculetype to decouple<br>
couple-lambda0 = vdw ; only van der Waals interactions<br>
couple-lambda1 = none ; turn off everything, in this case only vdW<br>
couple-intramol = no<br>
nstdhdl = 10<br>
; Do not generate velocities<br>
gen_vel = no<br>
; options for bonds<br>
constraints = h-bonds ; we only have C-H bonds here<br>
; Type of constraint algorithm<br>
constraint-algorithm = lincs<br>
; Constrain the starting configuration<br>
; since we are continuing from NPT<br>
continuation = yes<br>
; Highest order in the expansion of the constraint coupling matrix<br>
lincs-order = 12<br>
<br>
<br></div></div>
1 Þubat 2012 19:41 tarihinde 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>>> yazdý:<div><div class="h5">
<br>
<br>
<br>
<br>
mehmet kýytak wrote:<br>
<br>
hi all...<br>
ý have a problem.. ý got segmentation fault when run nvt<br>
equilibration.. ý use below mdp file<br>
<br>
<br>
Please post a complete .mdp file. The Unix 'cat' command can be<br>
used to print the contents of the text file, which can then be<br>
copied and pasted into an email.<br>
<br>
<br>
<br>
couple-lambda0 = vdw ; only van der Waals<br>
interactions<br>
couple-lambda1 = none ; turn off everything, in<br>
this case only vdW<br>
couple-intramol = no<br>
nstdhdl = 10<br>
<br>
<br>
It appears you are trying to do a free energy calculation by<br>
transforming your system. Turn off the free energy code to<br>
determine whether or not this is a source of the problem.<br>
<br>
<snip><br>
<br>
<br>
Step 3, time 0.006 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.337002, max 0.559171 (between atoms 1 and 4)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
1 2 90.0 0.1006 0.1091 0.1000<br>
1 3 90.0 0.2058 0.1141 0.1000<br>
1 4 90.0 0.3028 0.1559 0.1000<br>
<br>
Back Off! I just backed up step3b_n3.pdb to ./#step3b_n3.pdb.1#<br>
<br>
Back Off! I just backed up step3b_n4.pdb to ./#step3b_n4.pdb.1#<br>
<br>
Back Off! I just backed up step3c_n2.pdb to ./#step3c_n2.pdb.1#<br>
<br>
Back Off! I just backed up step3c_n3.pdb to ./#step3c_n3.pdb.1#<br>
<br>
Back Off! I just backed up step3c_n4.pdb to ./#step3c_n4.pdb.1#<br>
Wrote pdb files with previous and current coordinates<br>
Wrote pdb files with previous and current coordinates<br>
Wrote pdb files with previous and current coordinates<br>
Segmentation fault<br>
mkiytak@babil:~<br>
<br>
PLEASE HELP ME...<br>
<br>
<br>
LINCS warnings are the most common error reported to this list.<br>
Please refer to the following pages for help:<br>
<br></div></div>
<a href="http://www.gromacs.org/__Documentation/Errors#LINCS.__2fSETTLE.2fSHAKE_warnings" target="_blank">http://www.gromacs.org/__<u></u>Documentation/Errors#LINCS.__<u></u>2fSETTLE.2fSHAKE_warnings</a><div class="im">
<br>
<<a href="http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors#LINCS.<u></u>2fSETTLE.2fSHAKE_warnings</a>><br>
<br>
If you still can't find your answer, refer to the list archive. As<br>
I said, such errors are commonly reported. Surely you'll find<br>
something useful. The only thing that can be said right now is that<br>
your system is unstable. Either you need better minimization or<br>
equilibration (or both), your .mdp settings are incorrect, or the<br>
free energy code is causing an instability (which is a symptom of<br>
the first two points, it does not suggest the free energy code is<br>
not working).<br>
<br>
-Justin<br>
<br></div>
-- ==============================<u></u>__==========<div class="im"><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>
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<br>
-- <br>
==============================<u></u>==========<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> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
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