[gmx-users] "Range checking error" issue

[Matteo Guglielmi]

David van der Spoel wrote:
> Matteo Guglielmi wrote:
>> Mark Abraham wrote:
>>> Matteo Guglielmi wrote:
>>>> I did what you suggest and even more, I decreased the timestep to
>>>> 0.001
>>>>
>>>> Well the problem doesn't go away.
>>>>
>>>> I've been reading mails from this discussion list... I'm not the only
>>>> who's experiencing this kind of problem (ci variable range error)...
>>>> actually few gmx users suggest it comes only from parallel runs which
>>>> is my case BTW.
>>> I've seen it most often when equilibration hasn't happened properly,
>>> but you'd think 1.5ns would be enough to avoid a crash.
>>>
>>>> I'm running parallel runs on different clusters... it's happening
>>>> everywhere.
>>> Do serial runs do it?
>>>
>>> Have you looked at your trajectory visually to see where things start
>>> going wrong?
>>>
>>> Mark
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>> I did no try any serial run yet... trajectory looks fine... but log
>> files might explain
>> why parallel runs keep crashing.
>>
>> Usually I run gromacs on a dual  Xeon 5140 cpus machine (2x2-cores) in
>> double precision.
>>
>> I did compile gromacs using the intel compilers - 9.1 series:
>>  
>> [matteo at lcbcpc02 ~]$ icc -V
>> Intel(R) C Compiler for Intel(R) EM64T-based applications, Version
>> 9.1    Build 20070320 Package ID: l_cc_c_9.1.049
>> Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.
>>
>> [matteo at lcbcpc02 ~]$ icpc -V
>> Intel(R) C++ Compiler for Intel(R) EM64T-based applications, Version
>> 9.1    Build 20070320 Package ID: l_cc_c_9.1.049
>> Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.
>>
>> [matteo at lcbcpc02 ~]$ ifort -V
>> Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version
>> 9.1    Build 20070320 Package ID: l_fc_c_9.1.045
>> Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.
>>
> an't post? Read http://www.gromacs.org/mailing_lists/users.php
> try again with gcc in that case. if that gives the same behavior then
> please submit a bugzilla.
>

I did post here (gmx-users-list) because the problem I'm currently
experiencing
with gromacs could be related to my input file set-up... anyway, you are
right.

What I noticed right now in my simulation is that the volume of the box
shrinks.
(water molecules not equilibrated)

I've also noticed that among the tree coordinates, z shrinks a bit
faster than x and y.

>From this point of view things seem to be much more clear to me i.e.
since the z
coordinates is shrinking, the Grid size gets updated to the new value
10x12x12
(initial value was 10x12x13!!!).

This might lead to the "Range checking error" if this situation is not
handled
properly by the gmx code.

MG.