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On 26/01/2012 5:10 PM, Alex Seling wrote:
<blockquote
cite="mid:CAHq4TGQRZW6kWhMLrmT9msczbWp0-nBt3uacpL--7j-P2owqVg@mail.gmail.com"
type="cite">
<div>Hello,<br>
<br>
After upgrading to gromacs 4.5.5, the old .mdp file that was
working is now giving me errors.</div>
</blockquote>
<br>
Marginally stable numerical integration can work out, or not. Here,
you are using a time step that is not suitable for a simulation
lacking bond constraints. See section 6.5 of manual, for example. If
you really want infinite cut-offs, read 7.3.9. Normal practice to
avoid problems is to use an equilibration regime whose integration
scheme is more gentle than your simulation regime.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAHq4TGQRZW6kWhMLrmT9msczbWp0-nBt3uacpL--7j-P2owqVg@mail.gmail.com"
type="cite">
<div> Specifically, I'm getting </div>
<div>"This usually means your system is exploding,</div>
<div>if not, you should increase table-extension in your mdp file</div>
<div>or with user tables increase the table size" <br>
for a few interactions, with each of them approaching inf.<br>
<br>
</div>
<div>This is with a good starting configuration. Any ideas as to
the error? My .mdp file is below.</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Alex Seling</div>
<div><br>
</div>
<div><br>
</div>
<div>title = lea at 300K</div>
<div>cpp = /lib/cpp -traditional</div>
<div>integrator = md ;sd ;md ;bd</div>
<div>tinit = 0.0</div>
<div>dt = 0.001 ;time step of 1 fs</div>
<div>nsteps = 238000000 ;1 us @ 1fs</div>
<div>nstxout = 200000 ; frequency to write coordinates to output
trajectory file = 1ns</div>
<div>nstxtcout = 200000 ; frequency to write coordinates to xtc
trajectory = 1 ns</div>
<div>
nstvout = 0</div>
<div>nstfout = 0</div>
<div>nstlog = 200000 ; frequency to write energies to log file = 1
ns</div>
<div>nstenergy = 200000 ; frequency to write energies to energy
file = 1ns</div>
<div>energygrps = system</div>
<div>comm_mode = angular</div>
<div>nstcomm = 40</div>
<div>nstlist = 100</div>
<div>nstype = simple</div>
<div>pbc = no</div>
<div>rlist = 100</div>
<div>rgbradii = 100</div>
<div>coulombtype = cut-off</div>
<div>epsilon_r = 1 ; double check this is what we want</div>
<div>rcoulomb = 100</div>
<div>vdwtype = cut-off</div>
<div>rvdw = 100</div>
<div>tc-grps = system</div>
<div>tau_t = 0.01099</div>
<div>ref_t = 300</div>
<div>gen_vel = yes</div>
<div>gen_temp = 273</div>
<div>constraints = none</div>
<div>implicit_solvent = GBSA</div>
<div>gb_algorithm = OBC</div>
<div>gb_epsilon_solvent = 78</div>
<div><br>
</div>
<br>
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