[gmx-users] Compiling g_correlation

[Justin Lemkul]

On 4/27/16 4:49 PM, Jorge Fernández de Cossío Díaz wrote:
> Is there a way to do the conversion? Perhaps a combo of trjconv from 4.6.5
> and 3.3? I'm thinking about it but cannot figure out a combination to work.
>

No, because there's no magic -make_compatible_with_prehistoric_version argument 
:)  You have to recreate a .tpr using grompp.  That likely implies .mdp changes 
since options have changed, but likely such instructions are irrelevant for the 
purpose of analysis, so anything syntactically correct should work.

-Justin

> On Wed, Apr 27, 2016 at 4:38 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> 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
>>>>>>>>>>> --
>>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>>
>>>>>>>>>>> * Please search the archive at
>>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
>>> before
>>>>>>>>>>> posting!
>>>>>>>>>>>
>>>>>>>>>>> * Can't post? Read
>> http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>>>
>>>>>>>>>>> * For (un)subscribe requests visit
>>>>>>>>>>>
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>> or
>>>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>
>>>>>>>>>> * Please search the archive at
>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
>>> before
>>>>>>>>>> posting!
>>>>>>>>>>
>>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>>
>>>>>>>>>> * For (un)subscribe requests visit
>>>>>>>>>>
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>> or
>>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>> Gromacs Users mailing list
>>>>>>>
>>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>>>
>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>
>>>>>>> * For (un)subscribe requests visit
>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>> or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>
>>>>>
>>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

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

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