[gmx-users] Range checking error: only on double precision
jshultz at hydrogenathome.org
Wed Mar 18 01:42:43 CET 2009
I guess its the amber03 force field I'm having issues with. The
lysozyme tutorial works if I use -ff G43a2
On Tue, Mar 17, 2009 at 8:01 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Well, several tutorials use lysozyme, PDB 1AKI. I would also recommend not
> using ffamber if you are running automated tests, since there are quirks
> with requiring specific nomenclature (for lysine, histidine, terminal
> residues, etc).
> Jack Shultz wrote:
>> 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
>>> atoms present and an integer charge. Maybe single precision somehow
>>> overcame these topology problems, but I wouldn't trust any of the
>>>> 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
>>>> errors that give particles very high velocities you might end up with
>>>> 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
>>>> 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
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 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