[gmx-users] Compiling g_correlation

Wed Apr 27 21:22:31 CEST 2016

I got g_correlation compiled. Now I'm trying to use it on a trajectory
generated with Gromacs 4.6.5. I get the following error:

Reading file topol.tpr, VERSION 4.6.5 (single precision)

-------------------------------------------------------
Program g_correlation, VERSION 3.3.4
Source code file: tpxio.c, line: 1192

Fatal error:
reading tpx file (topol.tpr) version 83 with version 40 program
-------------------------------------------------------

Is there something I can do to fix this? Is it possible to convert a .tpr
from v4.6.5 to v3.3?

Obviously running the simulation again in gromacs 3.3 is my LAST option.

On Wed, Apr 27, 2016 at 3:20 PM, Jorge Fernández de Cossío Díaz <
j.cossio.diaz at gmail.com> wrote:

> Great! That fixed it.
> Just change the line "#include <fatal.h>"  in traj_stuff.h to "#include
> <gmx_fatal.h>".
> Thanks
>
> On Wed, Apr 27, 2016 at 2:48 PM, Jorge Fernández de Cossío Díaz <
> j.cossio.diaz at gmail.com> wrote:
>
>> Great! That fixed it.
>> Just change the line "#include <fatal.h>"  in traj_stuff.h to "#include
>> <gmx_fatal.h>".
>> Thanks
>>
>> On Wed, Apr 27, 2016 at 2:40 PM, Kutzner, Carsten <ckutzne at gwdg.de>
>> wrote:
>>
>>>
>>> > On 27 Apr 2016, at 19:42, Jorge Fernández de Cossío Díaz <
>>> j.cossio.diaz at gmail.com> wrote:
>>> >
>>> > I compiled gromacs 3.3.4, and pointed the g_correlation Makefile to its
>>> > directory, But compilation of g_correlation still complains that it
>>> can't
>>> > find "fatal.h". Any ideas?
>>> it has been renamed to gmx_fatal.h
>>>
>>> Carsten
>>> >
>>> > On Wed, Apr 27, 2016 at 1:21 PM, Jorge Fernández de Cossío Díaz <
>>> > j.cossio.diaz at gmail.com> wrote:
>>> >
>>> >> Okay, will try to compile using gromacs 3.3.
>>> >>
>>> >> But my simulation was run in 4.6.5. Will I be able to use
>>> g_correlation to
>>> >> analyze it?
>>> >>
>>> >> On Wed, Apr 27, 2016 at 1:17 PM, Jorge Fernández de Cossío Díaz <
>>> >> j.cossio.diaz at gmail.com> wrote:
>>> >>
>>> >>> Okay, will try to compile using gromacs 3.3.
>>> >>>
>>> >>> But my simulation was run in 4.6.5. Will I be able to use
>>> g_correlation
>>> >>> to analyze it?
>>> >>>
>>> >>> On Wed, Apr 27, 2016 at 11:09 AM, Sarath Chandra <
>>> >>> sarathchandradantu at gmail.com> wrote:
>>> >>>
>>> >>>> You have to use gromacs 3.3 and also will need lamboot and other
>>> >>>> dependencies. Let me know how you progress. I recently installed it
>>> >>>> On Apr 27, 2016 8:35 PM, "Jorge Fernández de Cossío Díaz" <
>>> >>>> j.cossio.diaz at gmail.com> wrote:
>>> >>>>
>>> >>>>> I'm trying to use g_correlation (
>>> >>>>> http://www.mpibpc.mpg.de/grubmueller/g_correlation) to compute the
>>> >>>>> correlations in a MD simulation. I am using GROMACS 5.1.2 and 4.6.5
>>> >>>> (have
>>> >>>>> both).
>>> >>>>>
>>> >>>>> When I try to compile g_correlation, I get this error:
>>> >>>>>
>>> >>>>> cc -O6 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
>>> >>>>> -malign-double -funroll-all-loops -I/usr/include/libxml2
>>> >>>>> -I/usr/X11R6/include  -I/opt/gromacs/4.6.5/include/gromacs    -c -o
>>> >>>>> g_correlation.o g_correlation.c
>>> >>>>> In file included from g_correlation.c:47:0:
>>> >>>>> traj_stuff.h:10:19: fatal error: fatal.h: No such file or directory
>>> >>>>> #include <fatal.h>
>>> >>>>>                   ^
>>> >>>>> compilation terminated.
>>> >>>>> make: *** [g_correlation.o] Error 1
>>> >>>>>
>>> >>>>>
>>> >>>>> Apparently g_correlation was written in the time of gromacs 3. Any
>>> >>>> ideas of
>>> >>>>> how to solve this (ideally without having to install/compile
>>> gromacs 3
>>> >>>> as
>>> >>>>> well).
>>> >>>>>
>>> >>>>> best
>>> >>>>> --
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