[gmx-users] LINCS Warning with MDRUN - Segmentation Fault
Hi I am getting the following error with mdrun. I have done a few things but the system complains of 1-4 interactions and gives LINCS warning if the constraints are not turned off in the mdp file. I also changed the fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I get 1-4 interaction table size error and then LINCS warning. The output of mdrun for one of these peptides is as follows. I am working on normal mode decoys of each peptide and many of the decoys have no problems with mdrun but some gives this error and Segmentation Fault. Please advice. Gaurav OUTPUT OF MDRUN Reading file md_1dsl.cl_nH_tir_00710.H_bf.tpr, VERSION 3.3 (single precision) Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.096062 (between atoms 879 and 882) rms 0.005336 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Output set 710 with rmsf= 1.614 of 1dsl.cl_nH_tir.pdb in water' 10 steps, 200.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.048269 (between atoms 879 and 882) rms 0.002486 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 895 896 33.7 0.1090 0.1092 0.1090 Step 13, time 0.026 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.001279 (between atoms 882 and 883) rms 0.69 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 882 883 32.9 0.1011 0.1011 0.1010 Step 14, time 0.028 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.001462 (between atoms 882 and 883) rms 0.68 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 882 883 34.0 0.1011 0.1011 0.1010 Step 15, time 0.03 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.001105 (between atoms 888 and 890) rms 0.70 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 882 883 31.8 0.1011 0.1010 0.1010 Step 16, time 0.032 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.001912 (between atoms 888 and 890) rms 0.96 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 882 883 31.2 0.1010 0.1008 0.1010 Step 20, time 0.04 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.700586 (between atoms 873 and 875) rms 0.023589 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 873 875 90.0 0.1091 0.1854 0.1090 876 878 90.0 0.1090 0.1724 0.1090 Step 21, time 0.042 (ps) LINCS WARNING relative constraint deviation after LINCS: max 29473624.00 (between atoms 873 and 875) rms 776989.562500 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 835 837 34.7 0.1335 0.1732 0.1335 837 838 37.4 0.1010 0.1346 0.1010 837 839 109.7 0.1449 692.1205 0.1449 839 840 111.1 0.1090 692.1713 0.1090 839 841 100.5 0.1529 692.0815 0.1529 839 846 106.7 0.1522 1817.9144 0.1522 841 842 41.8 0.1090 0.1504 0.1090 841 843 41.9 0.1090 0.1508 0.1090 841 844 37.8 0.1410 0.1823 0.1410 846 847 104.8 0.1229 1896.3798 0.1229 846 848 104.1 0.1335 13946.6553 0.1335 848 849 102.0 0.1010 12523.5713 0.1010 848 850 93.4 0.1449 32162.5566 0.1449 850 851 92.5 0.1090 31577.1289 0.1090 850 852 95.3 0.1529 35935.5234 0.1529 850 867 95.0 0.1523 138461.0938 0.1522 852 853 99.7 0.1090 6120.9419 0.1090 852 854 96.8 0.1090 6488.6191 0.1090 852 855 104.6 0.1510 6414.0713 0.1510 855 856 113.0 0.1400 1370.1686 0.1400 855 858 112.2 0.1400 1379.8882 0.1400 856 857 122.2 0.1080 281.0437 0.1080 856 860 121.8 0.1400 280.9830 0.1400 858 859 117.1 0.1080 268.9571 0.1080 858 862 121.6 0.1400 268.9104 0.1400 860 861 31.6 0.1080 0.1373 0.1080 862 863 35.4 0.1080 0.1427 0.1080 867 868 90.7 0.1229 144391.0938 0.1229 867 869 90.2 0.1335 291070.9688 0.1335 869 870 90.3 0.1010 301462.5000 0.1010 869 871 90.5 0.1450 352037.4375 0.1449 871 872 91.2 0.1092 39090.6250 0.1090 871 873 80.9 0.1534 224179.3750 0.1529 871 891 105.9 0.1523 63050.6406 0.1522 873 874 83.6 0.1106 194899.4531 0.1090 873 875 89.0 0.1854 3212625. 0.1090 873 876 110.5 0.1526 154736.1719 0.1529 876 877 83.1 0.1104 96243.8906 0.1090 876 878 62.5 0.1724 90734.6406 0.1090 876 879 80.3 0.1534 125826.9609 0.1529 879 880 103.7 0.1100 48631.2148 0.1090 879 881 103.6 0.1093 48326.8906 0.1090 879 882 87.6 0.1467 53880.1172 0.1463 882 883 117.6 0.1009 388.4776 0.1010 882 884 160.2 0.1339 765.5904 0.1340 884 885 67.9 0.1340 475.1604 0.1340 884 888 70.4 0.1339 475.1462 0.1340 885 886 41.1 0.1010 0.1340 0.1010 885 887 40.5 0.1010 0.1327 0.1010 888 889 36.7 0.1011 0.1255 0.1010 891 892 86.4 0.1230 26705.6504 0.1229 891 893 70.7 0.1337 25659.6777 0.1335 893 894 81.4 0.1010 5832.3770 0.1010 893 895 101.2 0.1449 6486.8506 0.1449 895 896
Re: [gmx-users] LINCS Warning with MDRUN - Segmentation Fault
Gaurav Chopra wrote: Hi I am getting the following error with mdrun. I have done a few things but the system complains of 1-4 interactions and gives LINCS warning if the constraints are not turned off in the mdp file. I also changed the fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I get 1-4 interaction table size error and then LINCS warning. The output of mdrun for one of these peptides is as follows. I am working on normal mode decoys of each peptide and many of the decoys have no problems with mdrun but some gives this error and Segmentation Fault. Please advice. you need to minimize better, but if your structures are really bad it won't help either (e.g. when you have a sidechain sticking through a ring) -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems installing gromacs in a different directory
Eduardo Martins Lopes wrote: Greetins fellow Gromacs Users, I come to thee because when I tried to install gromacs in a different directory without SU privileges I get the following error (the last few log lines) Do I need super-user privileges ? oppush.Tpo; exit 1; fi if cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/home/debora/gromacs/share/top\ -I/home/debora/fftw/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double -funroll-all-loops -MT topcat.o -MD -MP -MF .deps/topcat.Tpo -c -o topcat.o topcat.c; \ then mv -f .deps/topcat.Tpo .deps/topcat.Po; else rm -f .deps/topcat.Tpo; exit 1; fi if cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/home/debora/gromacs/share/top\ -I/home/debora/fftw/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double -funroll-all-loops -MT topshake.o -MD -MP -MF .deps/topshake.Tpo -c -o topshake.o topshake.c; \ then mv -f .deps/topshake.Tpo .deps/topshake.Po; else rm -f .deps/topshake.Tpo; exit 1; fi make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/cluster/debora/gromacs-3.3.1/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/cluster/debora/gromacs-3.3.1/src' make: *** [all-recursive] Error 1 FFTW was installed perfectly. Am I wrong or those files inside the /gromacs-3.3.1/src are installed in the /src directory ? I have tried almost all combinations of fftw and gromacs and the same error is displayed everytime... Thanks in advance this works fine, I do it all the time. Typically you should do ./configure --prefix=/home/joe/gromacs or wherever you want it to go. Eduardo Martins Lopes Physics Student Universidade Federal de São Carlos - Brazil Yahoo! Messenger com voz http://us.rd.yahoo.com/mail/br/tagline/messenger/*http://br.messenger.yahoo.com/whatsnew.php - Instale agora e faça ligações de graça. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] questions about implicit solvent simulation
Dear Linchen, As Mark already told you there is no implicit solvent implementation in GROMACS ! The reaction field and generalized reaction field options are corrections to the long range electrostatic interactions. If you want to use an different dielectric cosntant than one you have to specify it in the mdp file with the keywork epsilon. Check out the manual for this, it must be indicated. I want to do a implicit solvent MD simulation. I wonder whether gromacs can fullfill the goal, if so, which option should I choose for electrostatics, reaction field or generalized reaction field? And what rcoulomb value is appropriate? if not, could I do a energy minimization for my protein in an enviroment of dielectric constant other than 1? Thanks a lot for your attention:) XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS Warning with MDRUN - Segmentation Fault
On Mon, 17 Apr 2006 00:07:29 -0700 Gaurav Chopra [EMAIL PROTECTED] wrote: Hi I am getting the following error with mdrun. I have done a few things but the system complains of 1-4 interactions and gives LINCS warning if the constraints are not turned off in the mdp file. I also changed the fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I get 1-4 interaction table size error and then LINCS warning. The output of mdrun for one of these peptides is as follows. I am working on normal mode decoys of each peptide and many of the decoys have no problems with mdrun but some gives this error and Segmentation Fault. Please advice. The lincs warnning are on water molecules isn't it ??? XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimization Problem
On Mon, 17 Apr 2006 08:21:35 -0400 (EDT) Robson P. S. Peguin [EMAIL PROTECTED] wrote: Hi everybody, I'm trying to simulate an interfacial system using Gromacs. My simulation box has water in one side and hydrofluorocarbon in the other side. This system was successfully tested using DL-POLY simulation package previously. Also, the box containing pure hydrofluorocarbon worked fine using Gromacs. However, when I try an energy minimization simulation with the interfacial system, after a couple of steps (~400), the geometry of the hydrofluorocarbon changes. I mean, the molecules begin to lose bonds or atoms. It didn't collapse the box yet, but I can see from a visualization package that the molecules are distorted. I tried to decrease the timestep unsuccessfully. If you have any suggestions, I'll be happy to know them. You should check your topology: bond definition from what you describe lokks necessary. XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: questions about implicit solvent simulation
@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] . Can't post? Read http://www.gromacs.org/mailing_lists/users.php--David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596,75124 Uppsala, Swedenphone:46 18 471 4205fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se --Message: 3Date: Mon, 17 Apr 2006 10:49:09 +0200From: X.Periole [EMAIL PROTECTED]Subject: Re: [gmx-users] questions about implicit solvent simulation To: Discussion list for GROMACS users gmx-users@gromacs.orgMessage-ID: [EMAIL PROTECTED]Content-Type: text/plain; charset=gb2312; format=flowed Dear Linchen,As Mark already told you there is no implicit solventimplementation in GROMACS ! The reaction field andgeneralized reaction field options are corrections to thelong range electrostatic interactions. If you want to use an different dielectric cosntant thanone you have to specify it in the mdp file with thekeywork epsilon. Check out the manual for this, it mustbe indicated. I want to do a implicit solvent MD simulation. I wonder whether gromacs can fullfill the goal, if so,which option should I choose for electrostatics, reactionfield or generalized reaction field? And what rcoulombvalue is appropriate? if not, could I do a energy minimization for my protein in an enviroment ofdielectric constant other than 1? Thanks a lot for your attention:)XAvier--Message: 4 Date: Mon, 17 Apr 2006 10:53:12 +0200From: X.Periole [EMAIL PROTECTED]Subject: Re: [gmx-users] LINCS Warning with MDRUN - Segmentation FaultTo: Discussion list for GROMACS users gmx-users@gromacs.orgMessage-ID: [EMAIL PROTECTED]Content-Type: text/plain; charset=ISO-8859-1; format=flowed On Mon, 17 Apr 2006 00:07:29 -0700Gaurav Chopra [EMAIL PROTECTED] wrote: Hi I am getting the following error with mdrun. I have done a few things but the system complains of 1-4 interactions and gives LINCSwarning if the constraints are not turned off in the mdp file. I alsochanged the fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrunbut I get 1-4 interaction table size error and then LINCS warning. Theoutput of mdrun for one of these peptides is as follows. I am working onnormal mode decoys of each peptide and many of the decoys have no problemswith mdrun but some gives this error and Segmentation Fault. Please advice.The lincs warnning are on water molecules isn't it ??? XAvier--Message: 5Date: Mon, 17 Apr 2006 09:38:34 + (GMT)From: Osman Yogurtcu [EMAIL PROTECTED] Subject: [gmx-users] question on g_clusterTo: gmx-users@gromacs.orgMessage-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=us-asciiHi,Is it possible to use g_cluster to cluster NAMD2 trajectories?I am trying to use g_cluster to cluster my NAMD2 deriven trajectories. First, I converted my .dcd trajectory into .pdb format. Then, tried this: g_cluster -f mypdb.pdb -cl clusters.pdband it did not work. Later, I converted my .pdb to .xtc and tried:g_cluster -f myxtc.xtc -cl clusters.pdbdoes not work either. Should I include a Gromacs MD run specific .tpr topology file as well, though it is mentioned as optional input? I hope you can help me out,BestOsman N. YogurtcuCenter for Computational Biology and BioinformaticsResearch AssistantKoc University-- next part --An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060417/ce5b3aa1/attachment-0001.html-- Message: 6Date: Mon, 17 Apr 2006 11:52:07 +0200From: David van der Spoel [EMAIL PROTECTED]Subject: Re: [gmx-users] question on g_clusterTo: Osman Yogurtcu [EMAIL PROTECTED], Discussion list forGROMACS users gmx-users@gromacs.orgMessage-ID: [EMAIL PROTECTED]Content-Type: text/plain; charset=ISO-8859-1; format=flowedOsman Yogurtcu wrote: Hi, Is it possible to use g_cluster to cluster NAMD2 trajectories? I am trying to use g_cluster to cluster my NAMD2 deriven trajectories. First, I converted my .dcd trajectory into .pdb format. Then, tried this:g_cluster -f mypdb.pdb -cl clusters.pdb and it did not work. Later, I converted my .pdb to .xtc and tried:g_cluster -f myxtc.xtc -cl clusters.pdb does not work either. Should I include a Gromacs MD run specific .tpr topology file as well, though it is mentioned as optional input? I hope you can help me out,try using -s reference.pdb Best Osman N. Yogurtcu Center for Computational Biology and Bioinformatics Research Assistant Koc University ___ gmx-users
Re: [gmx-users] Implementing Radial Distance Constraints
Bob Johnson wrote: Hello everyone, My system consists of a carbon nanotube and various chemicals that adsorb to the tube. I would like to use radial distance constraints to enforce adsorbates to maintain a fixed distance away from the nanotube. These restraints must obey the relation R = sqrt (x^2 + y^2) = user defined constant. With this type of restraint the adsorbates are free to move along the z and circumferential directions (something that can not be done with normal position or distance restraints). I would like to add a restraint potential given by V = 1/2*k*(R-R0)^2 = 1/2*k*( sqrt(x^2+y^2) - R0)^2. Here R0 is the fixed radial distance. Is this difficult to implement in Gromacs? What file in the source code would I edit? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php please be more clear. if we assume your cnt is centered along the z-axis, given roughly by x^2+y^2 = d0. Am I correct in assuming that you want all other particles to have x^2+y^2 = d1, where d1 d0 ? -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] more x2top troubles
Steven Kirk wrote:
Hello,
First, let me thank all those who have contributed helpful suggestions
here in the past, especially DvS.
I am having major problems generating a topology using x2top that
contains valid data in the [bonds], [angles] and [dihedrals] sections.
The files I use can be downloaded here:
http://datavet.hv.se/personal/SK/sio.pdb
http://datavet.hv.se/personal/SK/sio.top.gz
http://datavet.hv.se/personal/SK/ffoplsaa.n2t
The PDB file contains a 711-atom silica cluster centered in a 6nm box,
with the surface passivated with H atoms except for 9 sites where the H
atoms have been removed (leaving, notionally, a deprotonated silanol
group). I intend to hand-edit the [atoms] section of my topology later
so I can give these O atoms a -1 charge, fill the box with water and add
9 Na+ ions to the system for charge neutrality, but the charge issue is
in the future ..
Having copied the FF.dat, ffoplsaa.{itp, rtp, atp}, ffoplsaanb.itp and
ffoplsaabon.itp files from the installation directory to the current
working directory, I edited the new types OS, OH and HO into the
ffoplsaanb.itp file, copying the data for opls_179, opls_154 and
opls_155 respectively and setting the charge field to 0.0.
Having done this, the command (Linux x86_64, Gromacs release version 3.3.1)
GMXLIB=. x2top -f sio.pdb -o sio.top -name SNP -param -debug
gives the topology file listed above.
The masses have been copied into the topology OK, but x2top generates a
[bonds] section that looks like this:
[ bonds ]
; aiaj functc0c1c2c3
1 421 1 1.56e-01 4.00e+05 1.56e-01 4.00e+05
i.e. it seems to ignore the [bondtype] information provided at the
bottom of the ffoplsbon.itp file (edited in by DvS) describing what a
SI-OS bond should be like. This doesn't match with my expectations,
because there seem to be 4 parameters present (two of which are the
defaults for the -kb command line option) when I expected two, namely
'b0' and 'kb' with values taken from the ffoplsaabon.itp file.
The [angles] and [dihedrals] sections are similarly broken (but the
latter might be because the [dihedraltypes] section right at the end of
ffoplsaabon.itp seems to have too few parameters listed? Can the
developers check this?)
I would greatly appreciate any advice from anyone on this list on how to
fix this. I have read and re-read the manual many times and have
searched the mailing lists, but can find no solution.
Are there any other 3rd-party tools in existence that can generate a
valid topology (calculating [bonds], [angles] and [dihedrals]
information) for non-organic systems with this number of atoms (possibly
even by translation from other MD software's topology files ?)
To the experts: Is there a way of using a topology file with at least a
valid [atoms] section to produce e.g. a .tpr run file, then feeding back
the .tpr file generated as an input to x2top in an attempt to get valid
[bonds], [angles] and [dihedrals] sections in a 2-pass approach? I have
attempted this, with no success ..
*VERY* many thanks in advance for any advice you can provide,
Steve Kirk
Maybe we can move this question to bugzilla, I have already opened one:
http://bugzilla.gromacs.org/show_bug.cgi?id=69
please upload the files there, and let's try to work towards a more
general x2top.
--
David.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
___
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[gmx-users] Building a peptide
Hello, I'm a new GROMACS user. Just a simple question: Can I use GROMACS to build a small peptide (6 residues), de novo? If so, how do I do this? Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Building a peptide
Arneh Babakhani wrote: Hello, I'm a new GROMACS user. Just a simple question: Can I use GROMACS to build a small peptide (6 residues), de novo? If so, how do I do this? no. use e.g. pymol Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS 3.3.1 installation on SGI (Irix)
Just as a test can you try compiling gromacs using gcc if it's installed on your origin? You might need to pass some flags to ./configure (see ./configre --help) to tell it to use gcc instead. I think I already have ANSI C compiler so I installed FFTW 3.1 before installing GROMACS as mentioned. I installed FFTW in both single as well as double precision mode as advised and it went through. cc-3316 cc: ERROR File = gmx_fft_fftw3.c, Line = 186 The expression must be a pointer to a complete object type. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS 3.3.1 installation on SGI (Irix): 2
Hi
Hi ALl
I read through some of the e-mails of B. Nataraj and Erik Lindahl for
similar problem on compiling of GROMACS 3.3.1 on SGI IRIX.
As my error also pointed to a problem in gmx_fft_fftw3.c, I replaced the
'void' with 'char' in the line 150 of the file, as suggested.
I got the errors exactly the same as B. Nataraj got after doing this
modification, which is listed at
http://www.gromacs.org/pipermail/gmx-users/2006-April/020969.html
The same error is given below. I could not understand how to fix this error
and run GROMACS successfully.
Dr. Erik Lindahl wrote that: As far as I can see that file is perfectly
valid ANSI C - there is no executable statement in the declaration section.
However, I still do not know how to fix this?
Please help.
Regards
Akshay
Error is given below:
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1031
A declaration cannot appear after an executable statement in a block.
static real core_frac=0.5 ;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1032
A declaration cannot appear after an executable statement in a block.
t_pargs pa[] = {
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1073
A declaration cannot appear after an executable statement in a block.
FILE *log;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1074
A declaration cannot appear after an executable statement in a block.
intnatoms,nlist,naa,idum,nbin;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1075
A declaration cannot appear after an executable statement in a block.
t_atomsatoms;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1076
A declaration cannot appear after an executable statement in a block.
rvec *x;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1077
A declaration cannot appear after an executable statement in a block.
matrix box;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1078
A declaration cannot appear after an executable statement in a block.
char title[256],grpname[256];
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1079
A declaration cannot appear after an executable statement in a block.
t_dlist*dlist;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1080
A declaration cannot appear after an executable statement in a block.
char **aa;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1081
A declaration cannot appear after an executable statement in a block.
bool bChi,bCorr,bSSHisto;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1082
A declaration cannot appear after an executable statement in a block.
bool bDo_rt, bDo_oh, bDo_ot, bDo_jc ;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1083
A declaration cannot appear after an executable statement in a block.
real dt=0, traj_t_ns;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1085
A declaration cannot appear after an executable statement in a block.
atom_idisize,*index;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1086
A declaration cannot appear after an executable statement in a block.
intndih,nactdih,nf;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1087
A declaration cannot appear after an executable statement in a block.
real **dih,*trans_frac,*aver_angle,*time;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1088
A declaration cannot appear after an executable statement in a block.
inti,j,**chi_lookup,*xity;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1090
A declaration cannot appear after an executable statement in a block.
t_filenm fnm[] = {
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1106
A declaration cannot appear after an executable statement in a block.
int npargs;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1107
A declaration cannot appear after an executable statement in a block.
t_pargs *ppa;
^
20 errors detected in the compilation of gmx_chi.c.
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1
(bu21)__
__
Akshay Patny
Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry
Research Institute of Pharmaceutical Sciences
University of Mississippi
University, MS 38677
E-mail: [EMAIL PROTECTED]
Tel: 662-915-1286 (office); Web: www.olemiss.edu
___
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
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[gmx-users] Re: Implementing Radial Distance Constraints
please be more clear. if we assume your cnt is centered along the z-axis, given roughly by x^2+y^2 = d0. Am I correct in assuming that you want all other particles to have x^2+y^2 = d1, where d1 d0 ? -- David. The molecules in my system adsorb to the tube's outer wall. They are not inside the tube. Typically, the adsorbates reside 3.5A above the nanotubes surface (a typical distance for molecules interacting via VdW with an aromatic molecule). I want to constrain molecules to always adopt a monolayer about the nanotube. Therefore, I want to put a constraint on certain atoms to reside 3.5A above the nanotube. Let's say my nanotube has a radius of 0.5A. I would then want to implement a potential given by V = 1/2 k (R-0.5A)^2 where R = sqrt(x^2+y^2). This way, the atoms are able to slide along the z and cirumferential directions. Bob ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Implementing Radial Distance Constraints
Bob Johnson wrote: please be more clear. if we assume your cnt is centered along the z-axis, given roughly by x^2+y^2 = d0. Am I correct in assuming that you want all other particles to have x^2+y^2 = d1, where d1 d0 ? -- David. The molecules in my system adsorb to the tube's outer wall. They are not inside the tube. Typically, the adsorbates reside 3.5A above the nanotubes surface (a typical distance for molecules interacting via VdW with an aromatic molecule). I want to constrain molecules to always adopt a monolayer about the nanotube. Therefore, I want to put a constraint on certain atoms to reside 3.5A above the nanotube. Let's say my nanotube has a radius of 0.5A. I would then want to implement a potential given by V = 1/2 k (R-0.5A)^2 where R = sqrt(x^2+y^2). This way, the atoms are able to slide along the z and cirumferential directions. That potential will attempt to drag the adsorbates down to the radius of the nanotube - vdW forces will oppose this and equilibrium will occur somewhere, but probably inside 3.5A. I think there are less perturbative ways of applying these constraints. A potential like half of Figure 4.1.3 in the gromacs manual would make more sense, only switching on when R 3.5+0.5+x for some small x that acknowledges that 3.5 is an average distance. That is V = 0 for R = R0 V = 0.5 k ( sqrt(x^2+y^2) - R0 ) ^2 for R R0 Since you expect R-R0 to be small, you might consider implementing the approximate potential V = 0.5 k ( R^2 - R0^2 ) for computational efficiency. As far as finding out what to change goes, you'll need to change grompp to recognize a new type of cylindrical constraint, and then provide a function that evaluates the potential. There are a bunch of directives that affect the function of distance and orientation restraints for MD which won't want to concern you, so I suggest using the code for angle restraints as a template to adapt to your purposes. In the gromacs src directory, grep angle_restraints */*.[ch] and also with */*/*.[ch] to find the headers and code sections where grompp interprets the .top file. That will give a clue for the names of relevant data structures and what needs to be added where. You will need to modify src/gmxlib/bondfree.c to add a new potential type - grepping for angres will help you find all the places you need to add the new function and the supporting structure to work out when it gets called. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Meaning of cut-off
Taeho Kim wrote: Dear. I would like to know meaning of cut-off. Read the appropriate sections of the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] XT3 porting
Hello, I am trying to port GROMACS 3.3.1 to the CRAY XT3, which is essentially an Opteron machine with the PGI compilers. I can get everything to compile, but when I run mdrun, I am randomly getting segmentation faults. This seems to happen no matter what input file I use. It happens in init_forcerec (line 1001), in add_gbond, and in solvent_check. Some times it runs fine. I am configuring with the following command: ./configure --with-fft=fftw3 --disable-nice --enable-mpi --program-suffix=_xt3 --enable-float --with-external-blas --with-external-lapack --disable-threads --prefix=/usr/local/packages/gromacs-3.3.1 I am wondering if anyone else has seen these types of problems and knows how to fix them. I have tried compiling the code without optimization, to no avail. Thanks in advance, Shawn Shawn T. Brown Senior Scientific Support Specialist Pittsburgh Supercomputing Center Carnegie Mellon University Pittsburgh Supercomputing Center Rm #369 Pittsburgh, PA 15213 [EMAIL PROTECTED] tel: 412-268-4635 Add me to your address book... Want a signature like this? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Meaning of cut-off
Dear Kim, I recommend to read the manual, too. GROMACS manual is very good. If you study more, check bibliography in the manual. http://www.gromacs.org/documentation/paper_manuals.php makoto -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Tuesday, April 18, 2006 10:56 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Meaning of cut-off Taeho Kim wrote: Dear. I would like to know meaning of cut-off. Read the appropriate sections of the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] XT3 porting
Shawn T. Brown wrote: Hello, I am trying to port GROMACS 3.3.1 to the CRAY XT3, which is essentially an Opteron machine with the PGI compilers. I can get everything to compile, but when I run mdrun, I am “randomly” getting segmentation faults. This seems to happen no matter what input file I use. It happens in init_forcerec (line 1001), in add_gbond, and in solvent_check. Some times it runs fine. I am configuring with the following command: ./configure --with-fft=fftw3 --disable-nice --enable-mpi --program-suffix=_xt3 --enable-float --with-external-blas --with-external-lapack --disable-threads --prefix=/usr/local/packages/gromacs-3.3.1 I am wondering if anyone else has seen these types of problems and knows how to fix them. I have tried compiling the code without optimization, to no avail. Thanks in advance, Shawn Hi Shawn, last time I tested the PGI compiler gave at most equal performance as the gcc compilers. I presume you could try compiling with gcc. From your mail it is not clear whether the problems occurs in parallel or in sequential execution of mdrun. Anyway it is of course difficult to debug remotely, e.g. line 1001 is force.c does not look very suspect. Shawn T. Brown /Senior Scientific Support Specialist/ *Pittsburgh** Supercomputing Center* Carnegie Mellon University Pittsburgh Supercomputing Center Rm #369 Pittsburgh, PA 15213 http://maps.yahoo.com/py/maps.py?Pyt=Tmapaddr=Rm+%23369csz=Pittsburgh%2C+PA+15213country=us [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] tel: 412-268-4635 /Add me to your address book.../ https://www.plaxo.com/add_me?u=47245762259v0=2235038k0=564267859 /Want a signature like this?/ http://www.plaxo.com/signature ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS 3.3.1 installation on SGI (Irix): 2
Akshay Patny wrote:
Hi
Hi ALl
I read through some of the e-mails of B. Nataraj and Erik Lindahl for
similar problem on compiling of GROMACS 3.3.1 on SGI IRIX.
As my error also pointed to a problem in gmx_fft_fftw3.c, I replaced the
'void' with 'char' in the line 150 of the file, as suggested.
I got the errors exactly the same as B. Nataraj got after doing this
modification, which is listed at
http://www.gromacs.org/pipermail/gmx-users/2006-April/020969.html
The same error is given below. I could not understand how to fix this error
and run GROMACS successfully.
Dr. Erik Lindahl wrote that: As far as I can see that file is perfectly
valid ANSI C - there is no executable statement in the declaration section.
However, I still do not know how to fix this?
there is a double semicolon on one of the lines before it. please remove
it and retry.
Please help.
Regards
Akshay
Error is given below:
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1031
A declaration cannot appear after an executable statement in a block.
static real core_frac=0.5 ;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1032
A declaration cannot appear after an executable statement in a block.
t_pargs pa[] = {
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1073
A declaration cannot appear after an executable statement in a block.
FILE *log;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1074
A declaration cannot appear after an executable statement in a block.
intnatoms,nlist,naa,idum,nbin;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1075
A declaration cannot appear after an executable statement in a block.
t_atomsatoms;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1076
A declaration cannot appear after an executable statement in a block.
rvec *x;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1077
A declaration cannot appear after an executable statement in a block.
matrix box;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1078
A declaration cannot appear after an executable statement in a block.
char title[256],grpname[256];
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1079
A declaration cannot appear after an executable statement in a block.
t_dlist*dlist;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1080
A declaration cannot appear after an executable statement in a block.
char **aa;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1081
A declaration cannot appear after an executable statement in a block.
bool bChi,bCorr,bSSHisto;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1082
A declaration cannot appear after an executable statement in a block.
bool bDo_rt, bDo_oh, bDo_ot, bDo_jc ;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1083
A declaration cannot appear after an executable statement in a block.
real dt=0, traj_t_ns;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1085
A declaration cannot appear after an executable statement in a block.
atom_idisize,*index;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1086
A declaration cannot appear after an executable statement in a block.
intndih,nactdih,nf;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1087
A declaration cannot appear after an executable statement in a block.
real **dih,*trans_frac,*aver_angle,*time;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1088
A declaration cannot appear after an executable statement in a block.
inti,j,**chi_lookup,*xity;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1090
A declaration cannot appear after an executable statement in a block.
t_filenm fnm[] = {
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1106
A declaration cannot appear after an executable statement in a block.
int npargs;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1107
A declaration cannot appear after an executable statement in a block.
t_pargs *ppa;
^
20 errors detected in the compilation of gmx_chi.c.
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1
(bu21)__
__
Akshay Patny
Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry
Research Institute of Pharmaceutical Sciences
University of Mississippi
University, MS 38677
E-mail: [EMAIL PROTECTED]
Tel: 662-915-1286 (office); Web: www.olemiss.edu
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David.
Re: [gmx-users] XT3 porting
Tom Joseph wrote: Providing a backtrace or two would really help. Given the exact same input files and run conditions, does it sometimes segfault and sometimes not? Does this happen on a login node (full glibc and such) or just the compute nodes (POSIX subset)? Separately, is it a better idea to use fftw2 since it supports MPI? No, gromacs now does the parallel FFT itself, and fftw3 is slightly faster. (Hopefully soon my Teragrid access will extend to bigben, so I'm especially interested in this...) --Tom On Apr 17, 2006, at 10:06 PM, Shawn T. Brown wrote: Hello, I am trying to port GROMACS 3.3.1 to the CRAY XT3, which is essentially an Opteron machine with the PGI compilers. I can get everything to compile, but when I run mdrun, I am “randomly” getting segmentation faults. This seems to happen no matter what input file I use. It happens in init_forcerec (line 1001), in add_gbond, and in solvent_check. Some times it runs fine. I am configuring with the following command: ./configure --with-fft=fftw3 --disable-nice --enable-mpi --program-suffix=_xt3 --enable-float --with-external-blas --with-external-lapack --disable-threads --prefix=/usr/local/packages/gromacs-3.3.1 I am wondering if anyone else has seen these types of problems and knows how to fix them. I have tried compiling the code without optimization, to no avail. Thanks in advance, Shawn ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
