[gmx-users] Compiling g_correlation

[Justin Lemkul]

On 4/27/16 1:17 PM, Jorge Fernández de Cossío Díaz 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?
>

You'll need a new .tpr file, at minimum.  The force fields that were supported 
were much more limited in those days and the organization was different.

If it's me doing it, I update the code.  Changing the location of some headers 
and perhaps some syntax of any external functions should not be that painful. 
You can grep for the location of all the functions in minutes.

-Justin

> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================