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 <tsje...@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 <gmegario...@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 <mssula...@gmail.com>* έγραψε: >> >> >> Από: sulatha M. S <mssula...@gmail.com> >> Θέμα: [gmx-users] micelle clustering >> Προς: "Discussion list for GROMACS users" <gmx-users@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@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 >> www interface or send it to >> gmx-users-requ...@gromacs.org<http://mc/compose?to=gmx-users-requ...@gromacs.org> >> . >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> -- >> >> gmx-users mailing list 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 >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > 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@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list 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 www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
