[gmx-users] Compiling g_correlation

[Mark Abraham]

Like Justin said, you'll need a new .tpr made by 3.3. Hopefully that is
possible. That doesn't mean you run another simulation in 3.3 ;-)

Mark

On Wed, Apr 27, 2016 at 9:22 PM Jorge Fernández de Cossío Díaz <
j.cossio.diaz at gmail.com> wrote:

> 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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