Hi Tsjerk,<br><br>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<br>make trjconv<br>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?<br>
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<p class="MsoPlainText"><span style="font-family: "Courier New";">make trjconv<br>
/bin/sh ../../libtool --tag=CC<span style="">
</span>--mode=compile cc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2
-I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\"<span style=""> </span>-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<br>
<span style=""> </span>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<br>
gmx_trjconv.c: In function ‘taw_pbc_cluster’:<br>
gmx_trjconv.c:91: error: ‘gmx_bool’ undeclared (first use in this
function)<br>
gmx_trjconv.c:91: error: (Each undeclared identifier is reported only
once<br>
gmx_trjconv.c:91: error: for each function it appears in.)<br>
gmx_trjconv.c:91: error: expected ‘;’ before ‘bClustered’<br>
gmx_trjconv.c:148: error: ‘bClustered’ undeclared (first use in this function)<br>
gmx_trjconv.c: In function ‘calc_pbc_cluster’:<br>
gmx_trjconv.c:214: error: ‘gmx_bool’ undeclared (first use in this
function)<br>
gmx_trjconv.c:214: error: expected ‘;’ before ‘bChanged’<br>
gmx_trjconv.c:220: error: ‘bMol’ undeclared (first use in this function)<br>
gmx_trjconv.c:220: error: ‘bTmp’ undeclared (first use in this function)<br>
gmx_trjconv.c:333: error: ‘bChanged’ undeclared (first use in this
function)<br>
gmx_trjconv.c: In function ‘put_residue_com_in_box’:<br>
gmx_trjconv.c:442: error: ‘t_atom’ has no member named ‘resind’<br>
gmx_trjconv.c:465: error: ‘t_atom’ has no member named ‘resind’<br>
gmx_trjconv.c:483: error: ‘t_atom’ has no member named ‘resind’<br>
gmx_trjconv.c: In function ‘do_trunc’:<br>
gmx_trjconv.c:542: error: ‘t_fileio’ undeclared (first use in this function)<br>
gmx_trjconv.c:542: error: ‘in’ undeclared (first use in this function)<br>
gmx_trjconv.c:544: error: ‘gmx_bool’ undeclared (first use in this
function)<br>
gmx_trjconv.c:544: error: expected ‘;’ before ‘bStop’<br>
gmx_trjconv.c:546: error: ‘gmx_off_t’ undeclared (first use in this
function)<br>
gmx_trjconv.c:546: error: expected ‘;’ before ‘fpos’<br>
gmx_trjconv.c:557: warning: passing argument 1 of ‘open_trn’ discards
qualifiers from pointer target type<br>
gmx_trjconv.c:564: error: ‘fpos’ undeclared (first use in this function)<br>
gmx_trjconv.c:565: error: ‘bStop’ undeclared (first use in this function)<br>
gmx_trjconv.c:566: error: ‘bOK’ undeclared (first use in this function)<br>
gmx_trjconv.c:568: warning: implicit declaration of function ‘gmx_ftell’<br>
gmx_trjconv.c:571: warning: implicit declaration of function ‘gmx_fseek’<br>
gmx_trjconv.c: In function ‘gmx_trjconv’:<br>
gmx_trjconv.c:758: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘bAppend’<br>
gmx_trjconv.c:758: error: ‘bAppend’ undeclared (first use in this
function)<br>
gmx_trjconv.c:758: error: ‘bSeparate’ undeclared (first use in this
function)<br>
gmx_trjconv.c:758: error: ‘bVels’ undeclared (first use in this function)<br>
gmx_trjconv.c:758: error: ‘bForce’ undeclared (first use in this
function)<br>
gmx_trjconv.c:758: error: ‘bCONECT’ undeclared (first use in this
function)<br>
gmx_trjconv.c:759: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘bCenter’<br>
gmx_trjconv.c:759: error: ‘bCenter’ undeclared (first use in this
function)<br>
gmx_trjconv.c:765: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘bRound’<br>
gmx_trjconv.c:765: error: ‘bRound’ undeclared (first use in this
function)<br>
gmx_trjconv.c:855: error: ‘t_trxstatus’ undeclared (first use in this
function)<br>
gmx_trjconv.c:855: error: ‘trxout’ undeclared (first use in this
function)<br>
gmx_trjconv.c:855: error: invalid operands to binary *<br>
gmx_trjconv.c:856: error: ‘status’ undeclared (first use in this
function)<br>
gmx_trjconv.c:856: error: invalid operands to binary *<br>
gmx_trjconv.c:878: error: ‘clust_status’ undeclared (first use in this
function)<br>
gmx_trjconv.c:878: error: invalid operands to binary *<br>
gmx_trjconv.c:885: error: ‘gmx_bool’ undeclared (first use in this
function)<br>
gmx_trjconv.c:885: error: expected ‘;’ before ‘bFit’<br>
gmx_trjconv.c:887: error: ‘gmx_rmpbc_t’ undeclared (first use in this
function)<br>
gmx_trjconv.c:887: error: expected ‘;’ before ‘gpbc’<br>
gmx_trjconv.c:888: error: expected ‘;’ before ‘bRmPBC’<br>
gmx_trjconv.c:889: error: expected ‘;’ before ‘bCopy’<br>
gmx_trjconv.c:890: error: expected ‘;’ before ‘bExec’<br>
gmx_trjconv.c:891: error: expected ‘;’ before ‘bHaveFirstFrame’<br>
gmx_trjconv.c:892: error: expected ‘;’ before ‘bSubTraj’<br>
gmx_trjconv.c:893: error: expected ‘;’ before ‘bWriteFrame’<br>
gmx_trjconv.c:900: error: expected ‘;’ before ‘bWarnCompact’<br>
gmx_trjconv.c:902: error: ‘output_env_t’ undeclared (first use in this
function)<br>
gmx_trjconv.c:902: error: expected ‘;’ before ‘oenv’<br>
gmx_trjconv.c:920: error: ‘oenv’ undeclared (first use in this function)<br>
gmx_trjconv.c:920: warning: passing argument 9 of ‘parse_common_args’ from
incompatible pointer type<br>
gmx_trjconv.c:920: error: too many arguments to function
‘parse_common_args’<br>
gmx_trjconv.c:935: error: ‘bSetBox’ undeclared (first use in this
function)<br>
gmx_trjconv.c:936: error: ‘bSetTime’ undeclared (first use in this
function)<br>
gmx_trjconv.c:937: error: ‘bSetPrec’ undeclared (first use in this
function)<br>
gmx_trjconv.c:938: error: ‘bSetUR’ undeclared (first use in this
function)<br>
gmx_trjconv.c:939: error: ‘bExec’ undeclared (first use in this function)<br>
gmx_trjconv.c:940: error: ‘bTimeStep’ undeclared (first use in this
function)<br>
gmx_trjconv.c:941: error: ‘bTDump’ undeclared (first use in this
function)<br>
gmx_trjconv.c:942: error: ‘bDropUnder’ undeclared (first use in this
function)<br>
gmx_trjconv.c:943: error: ‘bDropOver’ undeclared (first use in this
function)<br>
gmx_trjconv.c:944: error: ‘bTrans’ undeclared (first use in this
function)<br>
gmx_trjconv.c:945: error: ‘bSplit’ undeclared (first use in this
function)<br>
gmx_trjconv.c:948: warning: passing argument 1 of ‘nenum’ from incompatible
pointer type<br>
gmx_trjconv.c:949: error: ‘bFit’ undeclared (first use in this function)<br>
gmx_trjconv.c:950: error: ‘bFitXY’ undeclared (first use in this
function)<br>
gmx_trjconv.c:951: error: ‘bReset’ undeclared (first use in this
function)<br>
gmx_trjconv.c:952: error: ‘bPFit’ undeclared (first use in this function)<br>
gmx_trjconv.c:953: warning: passing argument 1 of ‘nenum’ from incompatible
pointer type<br>
gmx_trjconv.c:954: error: ‘bPBCWhole’ undeclared (first use in this
function)<br>
gmx_trjconv.c:955: error: ‘bPBCcomRes’ undeclared (first use in this
function)<br>
gmx_trjconv.c:956: error: ‘bPBCcomMol’ undeclared (first use in this
function)<br>
gmx_trjconv.c:957: error: ‘bPBCcomAtom’ undeclared (first use in this
function)<br>
gmx_trjconv.c:958: error: ‘bNoJump’ undeclared (first use in this
function)<br>
gmx_trjconv.c:959: error: ‘bCluster’ undeclared (first use in this
function)<br>
gmx_trjconv.c:960: error: ‘bPBC’ undeclared (first use in this function)<br>
gmx_trjconv.c:961: warning: passing argument 1 of ‘nenum’ from incompatible pointer
type<br>
gmx_trjconv.c:962: warning: passing argument 1 of ‘nenum’ from incompatible
pointer type<br>
gmx_trjconv.c:970: error: ‘bRmPBC’ undeclared (first use in this
function)<br>
gmx_trjconv.c:995: error: ‘bIndex’ undeclared (first use in this
function)<br>
gmx_trjconv.c:1002: error: ‘bNeedPrec’ undeclared (first use in this
function)<br>
gmx_trjconv.c:1018: error: ‘bSubTraj’ undeclared (first use in this
function)<br>
gmx_trjconv.c:1039: error: incompatible types in assignment<br>
gmx_trjconv.c:1049: error: ‘bTPS’ undeclared (first use in this function)<br>
gmx_trjconv.c:1058: warning: passing argument 1 of ‘read_tps_conf’ discards
qualifiers from pointer target type<br>
gmx_trjconv.c:1075: warning: implicit declaration of function
‘gmx_conect_generate’<br>
gmx_trjconv.c:1075: warning: assignment makes pointer from integer without a
cast<br>
gmx_trjconv.c:1077: error: ‘gpbc’ undeclared (first use in this function)<br>
gmx_trjconv.c:1077: warning: implicit declaration of function
‘gmx_rmpbc_init’<br>
gmx_trjconv.c:1121: warning: passing argument 1 of ‘read_first_frame’ from
incompatible pointer type<br>
gmx_trjconv.c:1121: warning: passing argument 2 of ‘read_first_frame’ from
incompatible pointer type<br>
gmx_trjconv.c:1121: warning: passing argument 3 of ‘read_first_frame’ from
incompatible pointer type<br>
gmx_trjconv.c:1121: warning: passing argument 4 of ‘read_first_frame’ makes
integer from pointer without a cast<br>
gmx_trjconv.c:1121: error: too many arguments to function
‘read_first_frame’<br>
gmx_trjconv.c:1124: warning: passing argument 1 of ‘close_trj’ makes integer
from pointer without a cast<br>
gmx_trjconv.c:1144: warning: implicit declaration of function ‘gmx_rmpbc’<br>
gmx_trjconv.c:1167: error: ‘t_atoms’ has no member named ‘resinfo’<br>
gmx_trjconv.c:1168: error: ‘t_atoms’ has no member named ‘resinfo’<br>
gmx_trjconv.c:1168: error: ‘t_atoms’ has no member named ‘resinfo’<br>
gmx_trjconv.c:1172: error: ‘t_atom’ has no member named ‘resind’<br>
gmx_trjconv.c:1172: warning: comparison between pointer and integer<br>
gmx_trjconv.c:1172: error: ‘t_atom’ has no member named ‘resind’<br>
gmx_trjconv.c:1172: warning: pointer/integer type mismatch in conditional
expression<br>
gmx_trjconv.c:1172: warning: assignment makes integer from pointer without a
cast<br>
gmx_trjconv.c:1187: error: ‘bHaveFirstFrame’ undeclared (first use in this
function)<br>
gmx_trjconv.c:1187: warning: passing argument 1 of ‘read_first_frame’ from
incompatible pointer type<br>
gmx_trjconv.c:1187: warning: passing argument 2 of ‘read_first_frame’ from
incompatible pointer type<br>
gmx_trjconv.c:1187: warning: passing argument 3 of ‘read_first_frame’ from
incompatible pointer type<br>
gmx_trjconv.c:1187: warning: passing argument 4 of ‘read_first_frame’ makes
integer from pointer without a cast<br>
gmx_trjconv.c:1187: error: too many arguments to function
‘read_first_frame’<br>
gmx_trjconv.c:1208: warning: implicit declaration of function
‘gmx_fexist’<br>
gmx_trjconv.c:1220: warning: passing argument 1 of ‘open_trx’ discards
qualifiers from pointer target type<br>
gmx_trjconv.c:1230: error: ‘bCopy’ undeclared (first use in this
function)<br>
gmx_trjconv.c:1249: warning: implicit declaration of function
‘trx_get_fileio’<br>
gmx_trjconv.c:1258: error: ‘bDTset’ undeclared (first use in this
function)<br>
gmx_trjconv.c:1303: error: ‘bDumpFrame’ undeclared (first use in this
function)<br>
gmx_trjconv.c:1337: warning: implicit declaration of function
‘gmx_rmpbc_trxfr’<br>
gmx_trjconv.c:1360: error: ‘bWriteFrame’ undeclared (first use in this
function)<br>
gmx_trjconv.c:1390: warning: implicit declaration of function
‘output_env_conv_time’<br>
gmx_trjconv.c:1390: warning: implicit declaration of function
‘output_env_get_time_unit’<br>
gmx_trjconv.c:1390: warning: format ‘%g’ expects type ‘double’, but argument 3
has type ‘int’<br>
gmx_trjconv.c:1390: warning: format ‘%s’ expects type ‘char *’, but argument 4
has type ‘int’<br>
gmx_trjconv.c:1393: error: ‘bDoIt’ undeclared (first use in this
function)<br>
gmx_trjconv.c:1408: warning: format ‘%8.3f’ expects type ‘double’, but argument
4 has type ‘int’<br>
gmx_trjconv.c:1441: error: ‘bWarnCompact’ undeclared (first use in this
function)<br>
gmx_trjconv.c:1489: error: ‘bSplitHere’ undeclared (first use in this
function)<br>
gmx_trjconv.c:1507: warning: passing argument 1 of ‘close_trx’ makes integer
from pointer without a cast<br>
gmx_trjconv.c:1515: error: incompatible types in assignment<br>
gmx_trjconv.c:1523: error: incompatible type for argument 1 of
‘write_trxframe’<br>
gmx_trjconv.c:1523: error: too many arguments to function
‘write_trxframe’<br>
gmx_trjconv.c:1528: error: incompatible type for argument 1 of
‘close_trx’<br>
gmx_trjconv.c:1537: warning: passing argument 1 of ‘write_trxframe’ makes integer
from pointer without a cast<br>
gmx_trjconv.c:1537: error: too many arguments to function
‘write_trxframe’<br>
gmx_trjconv.c:1562: error: too many arguments to function ‘write_pdbfile’<br>
gmx_trjconv.c:1611: error: ‘bHaveNextFrame’ undeclared (first use in this function)<br>
gmx_trjconv.c:1611: warning: passing argument 1 of ‘read_next_frame’ makes
integer from pointer without a cast<br>
gmx_trjconv.c:1611: warning: passing argument 2 of ‘read_next_frame’ from
incompatible pointer type<br>
gmx_trjconv.c:1611: error: too many arguments to function
‘read_next_frame’<br>
gmx_trjconv.c:1620: warning: passing argument 1 of ‘close_trj’ makes integer
from pointer without a cast<br>
gmx_trjconv.c:1622: warning: implicit declaration of function
‘gmx_rmpbc_done’<br>
gmx_trjconv.c:1625: warning: passing argument 1 of ‘close_trx’ makes integer
from pointer without a cast<br>
gmx_trjconv.c:1630: error: used struct type value where scalar is
required<br>
gmx_trjconv.c:1631: error: incompatible type for argument 1 of
‘close_trx’<br>
gmx_trjconv.c:1635: warning: passing argument 1 of ‘do_view’ from incompatible
pointer type<br>
gmx_trjconv.c:1635: warning: passing argument 2 of ‘do_view’ discards
qualifiers from pointer target type<br>
gmx_trjconv.c:1635: error: too many arguments to function ‘do_view’<br>
make: *** [gmx_trjconv.lo] Error 1<br>
</span></p>
<br>Thanks,<br>Sulatha<br><br><br><br><div class="gmail_quote">2011/6/30 Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Sulatha,<br><br>Did you install gromacs yourself or are you using a system wide installation?<br><br>A. I installed myself<br><br>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' <br>
<br>B. I just used what was available already<br><br>If you're good friends with the system administrator you can ask him/her to compile the modified trjconv, as under A.<br>Otherwise, you'd better install gromacs yourself as explained on the gromacs site and then go to A.<br>
<br>Hope it helps,<br><br>Tsjerk<br><br><div class="gmail_quote"><div><div></div><div class="h5">On Thu, Jun 30, 2011 at 10:10 AM, gregory megariotis <span dir="ltr"><<a href="mailto:gmegariotis@yahoo.gr" target="_blank">gmegariotis@yahoo.gr</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><table border="0" cellpadding="0" cellspacing="0">
<tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
Dear Sulatha, <br><br>You can try the command <span></span><span style="font-style: italic;">trjconv -f a.xtc -o
b.gro -pbc cluster -e 0.002</span> with GROMACS 4.5.4. <br><br>Best regrds <br><br>Grigoris<br><br>--- Στις <b>Πέμ., 30/06/11, ο/η sulatha M. S <i><<a href="mailto:mssulatha@gmail.com" target="_blank">mssulatha@gmail.com</a>></i></b> έγραψε:<br>
<blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>Από: sulatha M. S <<a href="mailto:mssulatha@gmail.com" target="_blank">mssulatha@gmail.com</a>><br>Θέμα: [gmx-users] micelle clustering<br>
Προς: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>Ημερομηνία: Πέμπτη, 30 Ιούνιος 2011, 9:18<div><div></div><div><br>
<br><div>
<p>Hi all,<br></p><p>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. <span> </span>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 </p>
<pre><a rel="nofollow" href="http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering" target="_blank">http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering</a></pre>
<p>and also looked at the various posts given on this topic, (specifically
Chris Neale’s and Tsjerk’s mails).</p>
<p>As posted by Chris Neale, I tried using the commands,</p>
<pre>1. trjconv -f a.xtc -o b.gro -pbc cluster -e 0.001 (make sure to just<span> </span></pre><pre>get one frame)</pre><pre>2. grompp -f a.mdp -c b.gro -p a.top -o b.tpr</pre><pre>3. trjconv -f a.xtc -o b.xtc -s b.tpr -pbc nojump</pre>
<p> </p>
<p>Also mentioned in Tsjerk’ post that</p>
<pre>“When doing so, be sure to use a frame which is close enough to the</pre><pre>starting frame in terms of the coordinates. -pbc nojump works based on</pre><pre>the coordinates and if you use a reference which doesn't match the</pre>
<pre>starting frame close enough everything can get really messed up”.</pre><pre> </pre><pre> </pre>
<p>I tried the command 1 with </p>
<p><span> </span>trjconv -f a.xtc -o
b.gro -pbc cluster -e 0.002 </p>
<p>and also</p>
<p><span> </span>trjconv -f a.xtc -o
b.gro -pbc cluster –dump X (where x=2, 4, 6, 8 etc..)</p>
<p>The program gets into a never ending loop. </p>
<p>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.</p>
<p>I will greatly appreciate any help on how to go about doing
this specifically which frame (for dump or –e argument) .<span> </span>Please guide me on this.</p>
<p>I also downloaded the modified trjconv.c<span> </span>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.</p><p><br></p><p>Thanks for any help or clue,<br></p><p>Sulatha</p><p><br></p>
</div><br></div></div>-----Ακολουθεί συνημμένο-----<br><br><div>-- <br>gmx-users mailing list <a href="http://mc/compose?to=gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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</blockquote></td></tr></tbody></table><br></div></div>--<div class="im"><br>
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<br>post-doctoral researcher<br>Molecular Dynamics Group<br>* Groningen Institute for Biomolecular Research and Biotechnology<br>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<br>
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