[gmx-users] Range checking error: only on double precision
jshultz at hydrogenathome.org
Wed Mar 18 00:56:43 CET 2009
Can you suggest any pdb files I could use that are more simple? I've
been trying to use files from tutorials but it seems like are always
On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Jack Shultz wrote:
>> I just wanted to compare results between single and double precision.
>> I reused the same parameters. Single works. Double caused errors on
>> mdrun. Any idea why?
> I don't know why any of that worked at all. You've got missing atoms and
> inconsistent naming (LYSH should be LYP if you really want a protonated
> lysine under the Amber ports, etc). Did you give pdb2gmx -missing?
> Otherwise, topology generation should have failed.
> Especially troublesome:
> System has non-zero total charge: -2.309866e+01
> I would suggest running tests on a physically realistic system that has all
> atoms present and an integer charge. Maybe single precision somehow
> overcame these topology problems, but I wouldn't trust any of the results.
>> Program mdrun, VERSION 4.0.3
>> Source code file: nsgrid.c, line: 357
>> Range checking error:
>> Explanation: During neighborsearching, we assign each particle to a grid
>> based on its coordinates. If your system contains collisions or parameter
>> errors that give particles very high velocities you might end up with some
>> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
>> put these on a grid, so this is usually where we detect those errors.
>> Make sure your system is properly energy-minimized and that the potential
>> energy seems reasonable before trying again.
>> Variable ci has value -2147483648. It should have been within [ 0 .. 300 ]
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users