[gmx-users] micelle clustering

[sulatha M. S]

Hi Tsjerk,

I installed gromacs myself. I put the modified gmx_trjconv.c code in the
/src/tools subdirectory where the source code is located and tried the
command
make trjconv
But it gives me a series of error messages, as given below. My gromacs
version is 4.0.7. I would like to continue in this version till I finish the
set of runs which I have been doing before moving into 4.5.4 version. or
else can I do the analysis alone in gromacs 4.5.4 with the xtc files
generated from 4.0.7 version?

make trjconv
/bin/sh ../../libtool --tag=CC   --mode=compile cc -DHAVE_CONFIG_H -I.
-I../../src -I/usr/include/libxml2 -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\"   -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_trjconv.lo
-MD -MP -MF .deps/gmx_trjconv.Tpo -c -o gmx_trjconv.lo gmx_trjconv.c
 cc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_trjconv.lo
-MD -MP -MF .deps/gmx_trjconv.Tpo -c gmx_trjconv.c -o gmx_trjconv.o
gmx_trjconv.c: In function 'taw_pbc_cluster':
gmx_trjconv.c:91: error: 'gmx_bool' undeclared (first use in this function)
gmx_trjconv.c:91: error: (Each undeclared identifier is reported only once
gmx_trjconv.c:91: error: for each function it appears in.)
gmx_trjconv.c:91: error: expected ';' before 'bClustered'
gmx_trjconv.c:148: error: 'bClustered' undeclared (first use in this
function)
gmx_trjconv.c: In function 'calc_pbc_cluster':
gmx_trjconv.c:214: error: 'gmx_bool' undeclared (first use in this function)
gmx_trjconv.c:214: error: expected ';' before 'bChanged'
gmx_trjconv.c:220: error: 'bMol' undeclared (first use in this function)
gmx_trjconv.c:220: error: 'bTmp' undeclared (first use in this function)
gmx_trjconv.c:333: error: 'bChanged' undeclared (first use in this function)
gmx_trjconv.c: In function 'put_residue_com_in_box':
gmx_trjconv.c:442: error: 't_atom' has no member named 'resind'
gmx_trjconv.c:465: error: 't_atom' has no member named 'resind'
gmx_trjconv.c:483: error: 't_atom' has no member named 'resind'
gmx_trjconv.c: In function 'do_trunc':
gmx_trjconv.c:542: error: 't_fileio' undeclared (first use in this function)
gmx_trjconv.c:542: error: 'in' undeclared (first use in this function)
gmx_trjconv.c:544: error: 'gmx_bool' undeclared (first use in this function)
gmx_trjconv.c:544: error: expected ';' before 'bStop'
gmx_trjconv.c:546: error: 'gmx_off_t' undeclared (first use in this
function)
gmx_trjconv.c:546: error: expected ';' before 'fpos'
gmx_trjconv.c:557: warning: passing argument 1 of 'open_trn' discards
qualifiers from pointer target type
gmx_trjconv.c:564: error: 'fpos' undeclared (first use in this function)
gmx_trjconv.c:565: error: 'bStop' undeclared (first use in this function)
gmx_trjconv.c:566: error: 'bOK' undeclared (first use in this function)
gmx_trjconv.c:568: warning: implicit declaration of function 'gmx_ftell'
gmx_trjconv.c:571: warning: implicit declaration of function 'gmx_fseek'
gmx_trjconv.c: In function 'gmx_trjconv':
gmx_trjconv.c:758: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'bAppend'
gmx_trjconv.c:758: error: 'bAppend' undeclared (first use in this function)
gmx_trjconv.c:758: error: 'bSeparate' undeclared (first use in this
function)
gmx_trjconv.c:758: error: 'bVels' undeclared (first use in this function)
gmx_trjconv.c:758: error: 'bForce' undeclared (first use in this function)
gmx_trjconv.c:758: error: 'bCONECT' undeclared (first use in this function)
gmx_trjconv.c:759: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'bCenter'
gmx_trjconv.c:759: error: 'bCenter' undeclared (first use in this function)
gmx_trjconv.c:765: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'bRound'
gmx_trjconv.c:765: error: 'bRound' undeclared (first use in this function)
gmx_trjconv.c:855: error: 't_trxstatus' undeclared (first use in this
function)
gmx_trjconv.c:855: error: 'trxout' undeclared (first use in this function)
gmx_trjconv.c:855: error: invalid operands to binary *
gmx_trjconv.c:856: error: 'status' undeclared (first use in this function)
gmx_trjconv.c:856: error: invalid operands to binary *
gmx_trjconv.c:878: error: 'clust_status' undeclared (first use in this
function)
gmx_trjconv.c:878: error: invalid operands to binary *
gmx_trjconv.c:885: error: 'gmx_bool' undeclared (first use in this function)
gmx_trjconv.c:885: error: expected ';' before 'bFit'
gmx_trjconv.c:887: error: 'gmx_rmpbc_t' undeclared (first use in this
function)
gmx_trjconv.c:887: error: expected ';' before 'gpbc'
gmx_trjconv.c:888: error: expected ';' before 'bRmPBC'
gmx_trjconv.c:889: error: expected ';' before 'bCopy'
gmx_trjconv.c:890: error: expected ';' before 'bExec'
gmx_trjconv.c:891: error: expected ';' before 'bHaveFirstFrame'
gmx_trjconv.c:892: error: expected ';' before 'bSubTraj'
gmx_trjconv.c:893: error: expected ';' before 'bWriteFrame'
gmx_trjconv.c:900: error: expected ';' before 'bWarnCompact'
gmx_trjconv.c:902: error: 'output_env_t' undeclared (first use in this
function)
gmx_trjconv.c:902: error: expected ';' before 'oenv'
gmx_trjconv.c:920: error: 'oenv' undeclared (first use in this function)
gmx_trjconv.c:920: warning: passing argument 9 of 'parse_common_args' from
incompatible pointer type
gmx_trjconv.c:920: error: too many arguments to function 'parse_common_args'
gmx_trjconv.c:935: error: 'bSetBox' undeclared (first use in this function)
gmx_trjconv.c:936: error: 'bSetTime' undeclared (first use in this function)
gmx_trjconv.c:937: error: 'bSetPrec' undeclared (first use in this function)
gmx_trjconv.c:938: error: 'bSetUR' undeclared (first use in this function)
gmx_trjconv.c:939: error: 'bExec' undeclared (first use in this function)
gmx_trjconv.c:940: error: 'bTimeStep' undeclared (first use in this
function)
gmx_trjconv.c:941: error: 'bTDump' undeclared (first use in this function)
gmx_trjconv.c:942: error: 'bDropUnder' undeclared (first use in this
function)
gmx_trjconv.c:943: error: 'bDropOver' undeclared (first use in this
function)
gmx_trjconv.c:944: error: 'bTrans' undeclared (first use in this function)
gmx_trjconv.c:945: error: 'bSplit' undeclared (first use in this function)
gmx_trjconv.c:948: warning: passing argument 1 of 'nenum' from incompatible
pointer type
gmx_trjconv.c:949: error: 'bFit' undeclared (first use in this function)
gmx_trjconv.c:950: error: 'bFitXY' undeclared (first use in this function)
gmx_trjconv.c:951: error: 'bReset' undeclared (first use in this function)
gmx_trjconv.c:952: error: 'bPFit' undeclared (first use in this function)
gmx_trjconv.c:953: warning: passing argument 1 of 'nenum' from incompatible
pointer type
gmx_trjconv.c:954: error: 'bPBCWhole' undeclared (first use in this
function)
gmx_trjconv.c:955: error: 'bPBCcomRes' undeclared (first use in this
function)
gmx_trjconv.c:956: error: 'bPBCcomMol' undeclared (first use in this
function)
gmx_trjconv.c:957: error: 'bPBCcomAtom' undeclared (first use in this
function)
gmx_trjconv.c:958: error: 'bNoJump' undeclared (first use in this function)
gmx_trjconv.c:959: error: 'bCluster' undeclared (first use in this function)
gmx_trjconv.c:960: error: 'bPBC' undeclared (first use in this function)
gmx_trjconv.c:961: warning: passing argument 1 of 'nenum' from incompatible
pointer type
gmx_trjconv.c:962: warning: passing argument 1 of 'nenum' from incompatible
pointer type
gmx_trjconv.c:970: error: 'bRmPBC' undeclared (first use in this function)
gmx_trjconv.c:995: error: 'bIndex' undeclared (first use in this function)
gmx_trjconv.c:1002: error: 'bNeedPrec' undeclared (first use in this
function)
gmx_trjconv.c:1018: error: 'bSubTraj' undeclared (first use in this
function)
gmx_trjconv.c:1039: error: incompatible types in assignment
gmx_trjconv.c:1049: error: 'bTPS' undeclared (first use in this function)
gmx_trjconv.c:1058: warning: passing argument 1 of 'read_tps_conf' discards
qualifiers from pointer target type
gmx_trjconv.c:1075: warning: implicit declaration of function
'gmx_conect_generate'
gmx_trjconv.c:1075: warning: assignment makes pointer from integer without a
cast
gmx_trjconv.c:1077: error: 'gpbc' undeclared (first use in this function)
gmx_trjconv.c:1077: warning: implicit declaration of function
'gmx_rmpbc_init'
gmx_trjconv.c:1121: warning: passing argument 1 of 'read_first_frame' from
incompatible pointer type
gmx_trjconv.c:1121: warning: passing argument 2 of 'read_first_frame' from
incompatible pointer type
gmx_trjconv.c:1121: warning: passing argument 3 of 'read_first_frame' from
incompatible pointer type
gmx_trjconv.c:1121: warning: passing argument 4 of 'read_first_frame' makes
integer from pointer without a cast
gmx_trjconv.c:1121: error: too many arguments to function 'read_first_frame'
gmx_trjconv.c:1124: warning: passing argument 1 of 'close_trj' makes integer
from pointer without a cast
gmx_trjconv.c:1144: warning: implicit declaration of function 'gmx_rmpbc'
gmx_trjconv.c:1167: error: 't_atoms' has no member named 'resinfo'
gmx_trjconv.c:1168: error: 't_atoms' has no member named 'resinfo'
gmx_trjconv.c:1168: error: 't_atoms' has no member named 'resinfo'
gmx_trjconv.c:1172: error: 't_atom' has no member named 'resind'
gmx_trjconv.c:1172: warning: comparison between pointer and integer
gmx_trjconv.c:1172: error: 't_atom' has no member named 'resind'
gmx_trjconv.c:1172: warning: pointer/integer type mismatch in conditional
expression
gmx_trjconv.c:1172: warning: assignment makes integer from pointer without a
cast
gmx_trjconv.c:1187: error: 'bHaveFirstFrame' undeclared (first use in this
function)
gmx_trjconv.c:1187: warning: passing argument 1 of 'read_first_frame' from
incompatible pointer type
gmx_trjconv.c:1187: warning: passing argument 2 of 'read_first_frame' from
incompatible pointer type
gmx_trjconv.c:1187: warning: passing argument 3 of 'read_first_frame' from
incompatible pointer type
gmx_trjconv.c:1187: warning: passing argument 4 of 'read_first_frame' makes
integer from pointer without a cast
gmx_trjconv.c:1187: error: too many arguments to function 'read_first_frame'
gmx_trjconv.c:1208: warning: implicit declaration of function 'gmx_fexist'
gmx_trjconv.c:1220: warning: passing argument 1 of 'open_trx' discards
qualifiers from pointer target type
gmx_trjconv.c:1230: error: 'bCopy' undeclared (first use in this function)
gmx_trjconv.c:1249: warning: implicit declaration of function
'trx_get_fileio'
gmx_trjconv.c:1258: error: 'bDTset' undeclared (first use in this function)
gmx_trjconv.c:1303: error: 'bDumpFrame' undeclared (first use in this
function)
gmx_trjconv.c:1337: warning: implicit declaration of function
'gmx_rmpbc_trxfr'
gmx_trjconv.c:1360: error: 'bWriteFrame' undeclared (first use in this
function)
gmx_trjconv.c:1390: warning: implicit declaration of function
'output_env_conv_time'
gmx_trjconv.c:1390: warning: implicit declaration of function
'output_env_get_time_unit'
gmx_trjconv.c:1390: warning: format '%g' expects type 'double', but argument
3 has type 'int'
gmx_trjconv.c:1390: warning: format '%s' expects type 'char *', but argument
4 has type 'int'
gmx_trjconv.c:1393: error: 'bDoIt' undeclared (first use in this function)
gmx_trjconv.c:1408: warning: format '%8.3f' expects type 'double', but
argument 4 has type 'int'
gmx_trjconv.c:1441: error: 'bWarnCompact' undeclared (first use in this
function)
gmx_trjconv.c:1489: error: 'bSplitHere' undeclared (first use in this
function)
gmx_trjconv.c:1507: warning: passing argument 1 of 'close_trx' makes integer
from pointer without a cast
gmx_trjconv.c:1515: error: incompatible types in assignment
gmx_trjconv.c:1523: error: incompatible type for argument 1 of
'write_trxframe'
gmx_trjconv.c:1523: error: too many arguments to function 'write_trxframe'
gmx_trjconv.c:1528: error: incompatible type for argument 1 of 'close_trx'
gmx_trjconv.c:1537: warning: passing argument 1 of 'write_trxframe' makes
integer from pointer without a cast
gmx_trjconv.c:1537: error: too many arguments to function 'write_trxframe'
gmx_trjconv.c:1562: error: too many arguments to function 'write_pdbfile'
gmx_trjconv.c:1611: error: 'bHaveNextFrame' undeclared (first use in this
function)
gmx_trjconv.c:1611: warning: passing argument 1 of 'read_next_frame' makes
integer from pointer without a cast
gmx_trjconv.c:1611: warning: passing argument 2 of 'read_next_frame' from
incompatible pointer type
gmx_trjconv.c:1611: error: too many arguments to function 'read_next_frame'
gmx_trjconv.c:1620: warning: passing argument 1 of 'close_trj' makes integer
from pointer without a cast
gmx_trjconv.c:1622: warning: implicit declaration of function
'gmx_rmpbc_done'
gmx_trjconv.c:1625: warning: passing argument 1 of 'close_trx' makes integer
from pointer without a cast
gmx_trjconv.c:1630: error: used struct type value where scalar is required
gmx_trjconv.c:1631: error: incompatible type for argument 1 of 'close_trx'
gmx_trjconv.c:1635: warning: passing argument 1 of 'do_view' from
incompatible pointer type
gmx_trjconv.c:1635: warning: passing argument 2 of 'do_view' discards
qualifiers from pointer target type
gmx_trjconv.c:1635: error: too many arguments to function 'do_view'
make: *** [gmx_trjconv.lo] Error 1

Thanks,
Sulatha



2011/6/30 Tsjerk Wassenaar <tsjerkw at gmail.com>

> Hi Sulatha,
>
> Did you install gromacs yourself or are you using a system wide
> installation?
>
> A. I installed myself
>
> In that case you go into the directory where you have put the gromacs
> source code and put the modified version of gmx_trjconv.c in the
> subdirectory src/tools. Then you go into that directory and type 'make
> trjconv'
>
> B. I just used what was available already
>
> If you're good friends with the system administrator you can ask him/her to
> compile the modified trjconv, as under A.
> Otherwise, you'd better install gromacs yourself as explained on the
> gromacs site and then go to A.
>
> Hope it helps,
>
> Tsjerk
>
> On Thu, Jun 30, 2011 at 10:10 AM, gregory megariotis <gmegariotis at yahoo.gr
> > wrote:
>
>> Dear Sulatha,
>>
>> You can try the command trjconv -f a.xtc -o b.gro -pbc cluster -e 0.002with GROMACS 4.5.4.
>>
>> Best regrds
>>
>> Grigoris
>>
>> --- Στις *Πέμ., 30/06/11, ο/η sulatha M. S <mssulatha at gmail.com>* έγραψε:
>>
>>
>> Από: sulatha M. S <mssulatha at gmail.com>
>> Θέμα: [gmx-users] micelle clustering
>> Προς: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Ημερομηνία: Πέμπτη, 30 Ιούνιος 2011, 9:18
>>
>>
>> Hi all,
>>
>> I have simulated a system of randomly dispersed surfactants in water using
>> gromacs (4.0.7) for about 100 ns MD. Micelles are formed after around 40 ns.
>>  I am using a time step of 0.002 fs with xtc files written every 500
>> steps. For analyzing the micellar properties, I tried the commands given in
>>
>> http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering
>>
>> and also looked at the various posts given on this topic, (specifically
>> Chris Neale's and Tsjerk's mails).
>>
>> As posted by Chris Neale, I tried using the commands,
>>
>> 1. trjconv -f a.xtc -o b.gro -pbc cluster -e 0.001 (make sure to just
>>
>> get one frame)
>>
>> 2. grompp -f a.mdp -c b.gro -p a.top -o b.tpr
>>
>> 3. trjconv -f a.xtc -o b.xtc -s b.tpr -pbc nojump
>>
>>
>>
>> Also mentioned in Tsjerk' post that
>>
>> "When doing so, be sure to use a frame which is close enough to the
>>
>> starting frame in terms of the coordinates. -pbc nojump works based on
>>
>> the coordinates and if you use a reference which doesn't match the
>>
>> starting frame close enough everything can get really messed up".
>>
>>
>>
>>
>>
>> I tried the command 1 with
>>
>>  trjconv -f a.xtc -o b.gro -pbc cluster -e 0.002
>>
>> and also
>>
>>  trjconv -f a.xtc -o b.gro -pbc cluster -dump X (where x=2, 4, 6, 8
>> etc..)
>>
>> The program gets into a never ending loop.
>>
>> I also tried the command 1 on a later part of the trajectory (after 40
>> ns), there also the program enters in a indefinite loop.
>>
>> I will greatly appreciate any help on how to go about doing this
>> specifically which frame (for dump or -e argument) .  Please guide me on
>> this.
>>
>> I also downloaded the modified trjconv.c  by Tsjerk (in one of his posts
>> on micelle clustering), but do not know where to incorporate this. I need
>> some help on how to use this modified trjconv code.
>>
>>
>> Thanks for any help or clue,
>>
>> Sulatha
>>
>>
>>
>> -----Ακολουθεί συνημμένο-----
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org<http://mc/compose?to=gmx-users@gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
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>> .
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>>
>>
>> --
>>
>> gmx-users mailing list    gmx-users at gromacs.org
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>> Please search the archive at
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>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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