I checked the initial coordinate file for overlapping atoms, but nothing found.<br>I checked the step*.pdb file written after each crash but did not really understand those coordinates, for the problematic molecules have MORE THAN 1 positions in those files. what does that mean?<br>
<br>I tried to reproduce the error on another computer, and it could be reproduced.<br><br>I think I should check the initial coordinate more thoroughly to find all likely problematic points. Would you please recommend a way for me to do that check?<br>
<br>Thanks<br>Trang<br><br><div class="gmail_quote">On Thu, Sep 30, 2010 at 5:38 PM, 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><div></div><div class="h5"><br>
<br>
Trang wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear gmx-users,<br>
I do a minimization run with this mdp:<br>
-----------------------------<br>
constraints = none<br>
;define = -DFLEX_SPC<br>
integrator = cg<br>
;nstcgsteep = 300<br>
emtol = 100.0<br>
emstep = 0.005<br>
dt = 0.001 ; ps !<br>
nsteps = 200000 ; total 200 ps.<br>
nstcomm = 100<br>
nstxout = 10000<br>
nstvout = 0<br>
nstfout = 0<br>
nstlog = 10000<br>
nstenergy = 1000<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 1.0<br>
rcoulomb = 1.0<br>
rvdw = 1.0<br>
coulombtype = PME ; Reaction-Field<br>
fourierspacing = 0.12<br>
pme_order = 4<br>
optimize_fft = yes<br>
;epsilon_r = 1.0<br>
; Berendsen temperature coupling is on in two groups<br>
Tcoupl = berendsen<br>
tc-grps = Protein SOL<br>
tau_t = 0.01 0.01<br>
ref_t = 310 310<br>
; Energy monitoring<br>
energygrps = Protein SOL<br>
; Isotropic pressure coupling is now on<br>
Pcoupl = berendsen<br>
Pcoupltype = isotropic<br>
tau_p = 0.25<br>
compressibility = 5.4e-5<br>
ref_p = 1.0<br>
; Generate velocites is off at 300 K.<br>
gen_vel = no<br>
;gen_temp = 300.0<br>
;gen_seed = 749261<br>
<br>
---------------------------<br>
and get the error, output like this:<br>
<br>
Polak-Ribiere Conjugate Gradients:<br>
Tolerance (Fmax) = 1.00000e+02<br>
Number of steps = 200000<br>
F-max = 4.69437e+04 on atom 2513<br>
F-Norm = 1.05294e+03<br>
<br>
<br>
step -1: Water molecule starting at atom 43372 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
<br>
...<br>
<br>
Fatal error:<br>
1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.<br>
This usually means that your system is not well equilibrated.<br>
--------------------------<br>
<br>
I did a successful run with another equivalent system (same protein sequence, same number of atoms), even with a LARGER TIMESTEP, 0.002 ps<br>
I found a lot of people encounter the same error, but in production run step. And in those cases, they're advised to minimize/equilibrate the system more thoroughly. What can I do to resolve this problem in MINIMIZATION step?<br>
<br>
</blockquote>
<br></div></div>
You likely have some unresolvable atomic clash(es) in your system that can't be energy-minimized. Check your structure around the location of the problematic water molecule to see if anything is overlapping.<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;">
Many thanks<br>
Trang<br>
<br>
</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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