Re: [gmx-users] histidine charges in ffopls.rtp
Dear Marius, Did you check the reference given for the FF? I assume the charges are from there. Ran. Marius Retegan wrote: Hello I would like to know what charges are in the ffopls.rtp in the case of HISA. In the data below, on the 3rd column are the charges from Gromacs and on the 4th column are the charges for the same residue from a personal communication of opls parameters from prof. Jorgensen. [ HISA ] ; HISD in OPLS terminology [ atoms ] Nopls_238 -0.500-0.5000 Hopls_2410.300 0.3000 CAopls_224B 0.140 0.1400 HAopls_1400.060 0.0600 CBopls_505 -0.297-0.0050 HB1opls_1400.060 0.0600 HB2opls_1400.060 0.0600 CGopls_508 -0.261 0.0150 ND1opls_503 -0.291-0.5700 HD1opls_5040.326 0.4200 CD2opls_5070.504-0.0150 HD2opls_1460.183 0.1150 CE1opls_5060.182 0.2950 HE1opls_1460.098 0.1150 NE2opls_511 -0.564-0.4900 Copls_2350.500 0.5000 Oopls_236 -0.500-0.5000 Thank you Marius Retegan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] stop mailing me
stop mailing me Marius Retegan [EMAIL PROTECTED] wrote: Hello I would like to know what charges are in the ffopls.rtp in the case of HISA. In the data below, on the 3rd column are the charges from Gromacs and on the 4th column are the charges for the same residue from a personal communication of opls parameters from prof. Jorgensen. [ HISA ] ; HISD in OPLS terminology [ atoms ] N opls_238 -0.500 -0.5000 H opls_241 0.300 0.3000 CA opls_224B 0.140 0.1400 HA opls_140 0.060 0.0600 CB opls_505 -0.297 -0.0050 HB1 opls_140 0.060 0.0600 HB2 opls_140 0.060 0.0600 CG opls_508 -0.261 0.0150 ND1 opls_503 -0.291 -0.5700 HD1 opls_504 0.326 0.4200 CD2 opls_507 0.504 -0.0150 HD2 opls_146 0.183 0.1150 CE1 opls_506 0.182 0.2950 HE1 opls_146 0.098 0.1150 NE2 opls_511 -0.564 -0.4900 C opls_235 0.500 0.5000 O opls_236 -0.500 -0.5000 Thank you Marius Retegan ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 - Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Creating .top, .gro, .ndx, .itp files for TIP5Pwater
Friends, I would like to simulate a box of water (TIP5P model), with 258 water molecules. When I tried to build up the .top, .gro and .ndx files using the command pdb2gmx -p -i -n -o -f tip5p_W.pdb, I got an error message : input/ output error, program aborted. MY input structure, ie, tip5p_W.pdb contains the co ordinates for the solvent box and therefore I dont need to solvate it again!! Could you suggest the exact way to build up thes files ( .top, .gro, .ndx, .itp ) with a starting structure (.pdb files)? regards, Jestin Mandumpal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: gmx-users Digest, Vol 43, Issue 49
What you want to do, a dynamic updating of the QM atoms is not implemented yet. The difficulty with such scheme is energy conservation and force conservation when translocating an atom from the MM into the QM region and vice versa. This is a difficult problem. However, there soluitons, see for instance Heyden, Lin and Truhlar (J. Phys. Chem. B 2007, 111, 2231-2241). Therefore, if such a dynamic partitioning is essential for your research, you could implement their ideas into gromacs. Gerrit Message: 1 Date: Mon, 12 Nov 2007 15:10:08 -0500 From: Tandia, Adama [EMAIL PROTECTED] Subject: [gmx-users] QMMM for element with unknown forcefield To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=US-ASCII Dear GMX users, I'm not very familiar with the QMMM implementation in Gromacs, but I have two questions. 1- I would like to run a MD simulation for glass materials that contain B and Sb based oxides. Both elements are known to be multivalent in the compositions that I'm interested. Is it possible to setup a QMMM that assigns a sphere where QMMM is performed with a fixed radius around Sb and B, and have the spheres to move with the assigned atoms during the simulation? This would be a sort of Learn-On-The-Fly method. 2- Has anyone successfully compiled Gromacs 3.3.2 with QMMM set to work with Gaussian or CPMD? If yes, can I request the details of the compilation procedure? Best wishes, Adama == Adama Tandia Modeling Simulation Corning INC USA Tel: 607 248 1036 Fax: 607 974 3405 www.corning.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Creating .top, .gro, .ndx, .itp files for TIP5Pwater
JMandumpal wrote: Friends, I would like to simulate a box of water (TIP5P model), with 258 water molecules. When I tried to build up the .top, .gro and .ndx files using the command pdb2gmx -p -i -n -o -f tip5p_W.pdb, I got an error message : input/ output error, program aborted. MY input structure, ie, tip5p_W.pdb contains the co ordinates for the solvent box and therefore I dont need to solvate it again!! Could you suggest the exact way to build up thes files ( .top, .gro, .ndx, .itp ) with a starting structure (.pdb files)? there are starting structures and topology in your share/gromacs/top dir. regards, Jestin Mandumpal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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 search the archive at http://www.gromacs.org/search before posting! 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] g-hbond and N acceptors
David, Thanks for your reply. NH2 groups that are not aromatic (amines) one accept Hbonds of course. However there is not so much chemical knowledge in the program, and to make matters worse, you can not select acceptors or donors separately. Of course amine groups with a lone electron pair can in principle accept H-bonds. But in the case of proteins, no such groups are found (except on a deprotonated Lys). Peptide groups in the backbone as well as carboxyamide groups on Asn and Gln have hybrid orbitals which makes their structure planar and prevents to accept H-bonds. In proteins at reasonable pH, only deprotonated aromatic nitrogens on His should be considered acceptors. The GROMOS and HBPLUS manuals agree on this. In HBPLUS there is an option to accept other nitrogens as acceptors (see below) but only in cases where the protonation of His and orientation of Asn and Gln are not determined. These nitrogens are not considered acceptors by themselves. I would like to hack a correction for this in the code. I guess I would have to simply change line 400 of gmx_hbond.c (3.3.1) with something like : (*top-atoms.atomtype[i])[0] == 'NR5') Does this look right ? What is the difference between atomtype and atomtypeB ? Cheers, Michel FROM THE HBPLUS MANUAL Acceptors : 1. O (ie Main Chain COs of recognised amino - not imino - acid residues) 2. CYH SG, CSS SG, ASP OD1, ASP OD2, GLU OE1, GLU OE2, HIS ND1, MET SD, ASN OD1, GLN OE1, SER OG, THR OG1, TYR OH 3. Recognised acceptors of non-standard recognised molecules 4. Oxygen atoms in HETATM molecules (including waters) Atoms that may act as both donors and acceptors under the -X or -x options : 1. HIS CD2, HIS CE1, ASN OD1, ASN ND2, GLN OE1, GLN NE2 -x Exchange the side-chains of Histidine, Glutamine and Asparagnine. These side-chains are difficult to resolve crystallographically with certainty, which is why there is the option of adding potential hydrogen bonds that would be formed if HIS CD2 was actually ND1, HIS CE1 was NE2 and the nitrogens and oxygens of the ASN / GLN amide groups were actually the other way round. (Default is not to do this.) -- == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] soft-core and coulomb transformation
Hi, The bug was indeed was I expected. I have fixed it for version 3.3.3. You might not notice it easily, since the direct space contribution is usually larger than the mesh part. But for a two particle system I got nan's. Berk. From: David Mobley [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] soft-core and coulomb transformation Date: Mon, 12 Nov 2007 16:17:36 -0800 Berk, But what do you mean with charging and discharging? Going one way or the other in lambda does not matter. What matters is if there are particles that have zero charge in the A-state topology, while they have a non-zero charge in the B-state topology. Sorry, what I mean by charging versus discharging is that charging is where the A state has zero charges and the B state has normal charges, and discharging is the reverse. So charging is the scenario you describe, and discharging is the reverse. David Berk. From: David Mobley [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: bharat v. adkar [EMAIL PROTECTED] CC: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] soft-core and coulomb transformation Date: Mon, 12 Nov 2007 10:26:37 -0800 Following up on this issue, discharging phenol in water appears to give the same results as charging phenol in water. In other words, so far the only cases for which there seem to be a problem are relative calculations (and so far I haven't looked at this for any other than Bharat's test cases). Bharat, be sure you submit a bugzilla and we'll see how things go from there. I may at some point try setting up some of my own relative free energy topologies and see if I see the same effects, but I'm not likely to have time for that for a couple days. Thanks, David _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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 _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] g_order in a micelle
Hello, I'm trying to get the order parameter of lipids in a micelle, so i've decided to make a script that makes a trjconv of individual lipids, with a fit to a structure that is aligned along the Z axis. Now that I have the trajectories, i'm trying to launch g_order. The problem is that it requiers a tpr file that I don't have. I have tried to generate one using a modified mdp, top, and gro file , but i get a semgentation error. Is it possible to get a Tpr from a Trr ? Or even better , is it possible to make a g_order with a defined vector instead of the three axis ? Thanks. -- Jonathan KHAO LISM-IBSM-CNRS 31 Chemin Joseph Aiguier 13402 Marseille Cedex 20 France [EMAIL PROTECTED] tel : 0616738391 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] tabulated bonded interactions
Dear all, Tabulated bonded interactions have been implemented in December 2006. I wanted to know if they can be used in GMX 3.3.2 or 3.3.3 (and how). I couldn't find a list of changes between 3.3.1 and 3.3.2 online, and even the updates from 3.2 to 3.3 are still under construction according to the web site: http://www.gromacs.org/index.php?option=com_contenttask=categorysectionid=4id=58Itemid=132 Thanks, Ran. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] g_order in a micelle
Problem solved, thanks ! Jonathan Khao wrote: Hello, I'm trying to get the order parameter of lipids in a micelle, so i've decided to make a script that makes a trjconv of individual lipids, with a fit to a structure that is aligned along the Z axis. Now that I have the trajectories, i'm trying to launch g_order. The problem is that it requiers a tpr file that I don't have. I have tried to generate one using a modified mdp, top, and gro file , but i get a semgentation error. Is it possible to get a Tpr from a Trr ? Or even better , is it possible to make a g_order with a defined vector instead of the three axis ? Thanks. you can use tpbconv with an index file to make a tpr for one lipid from your original tpr file. -- Jonathan KHAO LISM-IBSM-CNRS 31 Chemin Joseph Aiguier 13402 Marseille Cedex 20 France [EMAIL PROTECTED] tel : 0616738391 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] SGI Altix - mdrun_mpi
Hi guys Just installed gmx on a SGI Altix system (64-way): -- compiling mdrun with MPI support, single-precision export CPPFLAGS=-I/home/nferreira/bin/fftw-3.0.1/include export LDFLAGS=-L/home/nferreira/bin/fftw-3.0.1/lib ./configure --prefix=/home/nferreira/bin/gromacs-3.3.2 --enable-mpi --program-suffix=_mpi make mdrun make install-mdrun -- compiling all gromacs package programs without MPI, single-precision make distclean ./configure --prefix=/home/nferreira/bin/gromacs-3.3.2 make make install It runs fine on single nodes, but I can't put gmx running in parallel. The jobs are submitted directly (see a sample script bellow), without any queuing handler, like PBS. # This is my submission script ### lamboot -v hostfile lamnodes # Testing mpi mpirun -np 2 hello # GMX run grompp -np 2 -f equil -po equil_out -c after_em -p topology -o equil mpirun -np 2 mdrun_mpi -np 2 -deffnm equil -c after_equil lamhalt # This is hostfile file ### # My boot schema localhost cpu=64 I tryed several stuff (full paths for mpirun, mdrun_mpi, etc), but I'm always getting the same error. I also tested a hello program (from LAM-MPI user guide) and it gives no problems. Bellow is the output of the submission script: [EMAIL PROTECTED]:~/gmxbench ./script LAM 7.1.3/MPI 2 C++/ROMIO - Indiana University n-116608 ssi:boot:base:linear: booting n0 (localhost) n-116608 ssi:boot:base:linear: finished n0 localhost:64:origin,this_node Hello, world! I am 0 of 2 Hello, world! I am 1 of 2 NNODES=2, MYRANK=1, HOSTNAME=behemoth NNODES=2, MYRANK=0, HOSTNAME=behemoth NODEID=0 argc=8 NODEID=1 argc=8 :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.3.2 (-: [ ... snipped ...] Getting Loaded... Reading file equil.tpr, VERSION 3.3.2 (single precision) - One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a return 0 or exit(0) in your C code before exiting the application. PID 16623 failed on node n0 (127.0.0.1) due to signal 11. - LAM 7.1.3/MPI 2 C++/ROMIO - Indiana University Any ideas? Searching the mailing list, seems that this is a recurrent issue, but I was not able to find and answer. And, the machine admin is not proficient in MPI. Cheers, Nuno P.S. Other programs are running fine on this machine using the same LAM-MPI. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] SGI Altix - mdrun_mpi
I think that your host file is perhaps not correct. In any event, it is different than my usage. This is how I can run lam without a batch system: ssh n1 ./RunLam.sh ### $cat RunLam.sh PATH=$PATH:/dir/to/lam/bin:. LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/dir/to/lam/lib LAMRSH=ssh -x export LAMRSH PATH lamboot -v lamhosts /dir/to/lam/mpirun N /this/dir/mdrun.sh lamhalt ### $cat lamhosts n1 n2 n3 n4 Chris. ## Original message: Hi guys Just installed gmx on a SGI Altix system (64-way): -- compiling mdrun with MPI support, single-precision export CPPFLAGS=-I/home/nferreira/bin/fftw-3.0.1/include export LDFLAGS=-L/home/nferreira/bin/fftw-3.0.1/lib ./configure --prefix=/home/nferreira/bin/gromacs-3.3.2 --enable-mpi --program-suffix=_mpi make mdrun make install-mdrun -- compiling all gromacs package programs without MPI, single-precision make distclean ./configure --prefix=/home/nferreira/bin/gromacs-3.3.2 make make install It runs fine on single nodes, but I can't put gmx running in parallel. The jobs are submitted directly (see a sample script bellow), without any queuing handler, like PBS. # This is my submission script ### lamboot -v hostfile lamnodes # Testing mpi mpirun -np 2 hello # GMX run grompp -np 2 -f equil -po equil_out -c after_em -p topology -o equil mpirun -np 2 mdrun_mpi -np 2 -deffnm equil -c after_equil lamhalt # This is hostfile file ### # My boot schema localhost cpu=64 I tryed several stuff (full paths for mpirun, mdrun_mpi, etc), but I'm always getting the same error. I also tested a hello program (from LAM-MPI user guide) and it gives no problems. Bellow is the output of the submission script: nferreira at behemoth http://www.gromacs.org/mailman/listinfo/gmx-users:~/gmxbench ./script LAM 7.1.3/MPI 2 C++/ROMIO - Indiana University n-116608 ssi:boot:base:linear: booting n0 (localhost) n-116608 ssi:boot:base:linear: finished n0 localhost:64:origin,this_node Hello, world! I am 0 of 2 Hello, world! I am 1 of 2 NNODES=2, MYRANK=1, HOSTNAME=behemoth NNODES=2, MYRANK=0, HOSTNAME=behemoth NODEID=0 argc=8 NODEID=1 argc=8 :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.3.2 (-: [ ... snipped ...] Getting Loaded... Reading file equil.tpr, VERSION 3.3.2 (single precision) - One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a return 0 or exit(0) in your C code before exiting the application. PID 16623 failed on node n0 (127.0.0.1) due to signal 11. - LAM 7.1.3/MPI 2 C++/ROMIO - Indiana University Any ideas? Searching the mailing list, seems that this is a recurrent issue, but I was not able to find and answer. And, the machine admin is not proficient in MPI. Cheers, Nuno P.S. Other programs are running fine on this machine using the same LAM-MPI. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: SGI Altix - mdrun_mpi
Hi Chris, again ;-) I'm also running gromacs on another Cluster intel based ( using PBS), and my script submission procedure is similar to yours! Now, this new machine I'm trying to use is a SGI 64-way, thus I think that the lam nodes file is correct: 64 cpu's in a single node, or something like that. And, as you can see, the hello program does work on this machine when called from mpirun. As I told in my previous e-mail, there are people using the LAM-MPI on this machine, and in fact, the hostfile and part of the script submission file were written by my colleagues. Thus, I think that the hostfile is correct, and that probably something is not ok with the submission file, the gmx compilation (though the compilation was successful) or even with the system configuration. I tried also the suggestions in your script (exporting PATH, LD_LIBRARY_PATH, LAMRSH), but getting exactly the same error. Oh well ... Thanks for the reply, Nuno ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: SGI Altix - mdrun_mpi
Included with the things you recently tried did you use 'mpirun N mdrun -np 2' in place of 'mpirun -np 2 mdrun -np 2'? I'm certainly no expert, but it is a difference between our scripts. Otherwise I don't know. Perhaps recompile gromacs. Probably you have looked at this but did you check to see that yout .tpr file was created properly? Also you may want to try a 'sleep 10' between grompp and mdrun in case you have NFS delay issues. Good luck, Chris. ### original message Hi Chris, again ;-) I'm also running gromacs on another Cluster intel based ( using PBS), and my script submission procedure is similar to yours! Now, this new machine I'm trying to use is a SGI 64-way, thus I think that the lam nodes file is correct: 64 cpu's in a single node, or something like that. And, as you can see, the hello program does work on this machine when called from mpirun. As I told in my previous e-mail, there are people using the LAM-MPI on this machine, and in fact, the hostfile and part of the script submission file were written by my colleagues. Thus, I think that the hostfile is correct, and that probably something is not ok with the submission file, the gmx compilation (though the compilation was successful) or even with the system configuration. I tried also the suggestions in your script (exporting PATH, LD_LIBRARY_PATH, LAMRSH), but getting exactly the same error. Oh well ... Thanks for the reply, Nuno ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] make gives error in futil.c with mpi and ccc-6.5.6.002-1
I am having difficulty installing the mpi version of gromacs 3.3.2 on
a new computer. I have the same problems for 3.3.1. The serial version
appears to have worked fine. The cluster uses elan for MPI
I have parsed some values from config.log
configure:3291: ccc -V 5
Compaq C T6.5-002 on Linux 2.4.21-3.7qsnet alpha
Installed as ccc-6.5.6.002-1
Red Hat Linux release 7.2 (Enigma)
Using /usr/lib/gcc-lib/alpha-redhat-linux/2.96 (4).
Compiler Driver T6.5-001 (Linux) cc Driver
I believe my previous post was rejected since it was 2000 lines so I have put
the
entire config.log here: http://www.pomeslab.com/CN_GromacsPost_111407.html
and reposted.
mpicc appears to link like this (although the script is complicated enough
that I am not sure if this variable gets modified later):
my %mpilibs ='-L/usr/lib/mpi/mpi_compaq/lib -lmpifarg -lmpi -lelan'
I think that I must have autoconf somewhere since the Makefile was created,
however:
$automake --version
automake (GNU automake) 1.4-p5
$ autoconf --version
bash: autoconf: command not found
I have found some posts related to futil.c including the following
potential fix
http://www.gromacs.org/pipermail/gmx-users/2005-January/013806.html
but I didn't understand where the quotes were intended to go and the
next reply indicates that this is not a good idea in any event.
Another post indicates that I may be required to link it myself and
avoid the mpicc wrapper. I have tried including the following lines in
my compilation script before calling configure
export CC=gcc
export MPICC=gcc
export LIBS=-lmpi
but configure ends very quickly with the error message:
checking for C compiler default output file name... configure: error:
C compiler cannot create executables
Thanks for any assistance.
Chris.
I ran it like this:
#!/bin/bash
MD=/scratch/cneale/exe/gromacs-3.3.2
cd $MD
mkdir exec
export FFTW_LOCATION=/home/cneale/exe/fftw-3.1.2/exec
export GROMACS_LOCATION=${MD}/exec
export CPPFLAGS=-I$FFTW_LOCATION/include
export LDFLAGS=-L$FFTW_LOCATION/lib
./configure --prefix=$GROMACS_LOCATION --enable-mpi
--program-suffix=_mpi --disable-nice output.mpi_configure 21
make mdrun output.mpi_make_mdrun 21
make install-mdrun output.mpi_make_install_mdrun 21
#make distclean
The first error in the 'make mdrun' output is:
source='futil.c' object='futil.lo' libtool=yes \
DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H
-I. -I../../src -I../../include
-DGMXLIBDIR=\/scratch/cneale/exe/gromacs-3.3.2/exec/share/top\
-I/home/cneale/exe/fftw-3.1.2/exec/include -std1 -fast -O4 -no_ifo
-arch ev6 -unroll 2 -fp_reorder -c -o futil.lo futil.c
mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\/scratch/cneale/exe/gromacs-3.3.2/exec/share/top\
-I/home/cneale/exe/fftw-3.1.2/exec/include -std1 -fast -O4 -no_ifo
-arch ev6 -unroll 2 -fp_reorder -c futil.c -o futil.o
cc: Error: futil.c, line 521: Invalid expression. (badexpr)
strcpy(libpath,GMXLIBDIR);
-^
cc: Warning: futil.c, line 521: Invalid token discarded. (invaltoken)
strcpy(libpath,GMXLIBDIR);
-^
make[2]: *** [futil.lo] Error 1
make[2]: Leaving directory `/mnt/scratch/cneale/exe/gromacs-3.3.2/src/gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/scratch/cneale/exe/gromacs-3.3.2/src/gmxlib'
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Re: [gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1
[EMAIL PROTECTED] wrote:
I have had some success reproducing the event with a simple c program
and the issue appears to be with the in-house mpicc wrapper script. The
difference between gcc and mpicc appears limited to strings
(-D=\string\) and does not show up in numerical form (e.g. -D=4)
I'll post another update when the issue is resolved.
Chris.
In the following examples cc is the same as mpicc (they both point to a
script called 'compile') but mpicc invokes slightly different linking
options than cc
$ cat prog.c
#include stdlib.h
#include stdio.h
int main(int argn,char *args[]){
printf(The value of MYDEF is %s\n,MYDEF);
}
$ gcc prog.c -DMYDEF=\aaa\ -o prog
$ prog
The value of MYDEF is aaa
$ cc prog.c -DMYDEF=\aaa\ -o prog
cc: Error: prog.c, line 5: In this statement, aaa is not declared.
(undeclared)
printf(The value of MYDEF is %s\n,MYDEF);
--^
How about
cc prog.c '-DMYDEF=aaa' -o prog
###
However, when the defined value is a number, the problem dissapears:
$ cat prog_num.c
#include stdlib.h
#include stdio.h
int main(int argn,char *args[]){
printf(The value of MYDEF is %d\n,MYDEF);
}
$ gcc prog_num.c -DMYDEF=4 -o prog_num
$ prog_num
The value of MYDEF is 4
$ cc prog_num.c -DMYDEF=4 -o prog_num
$ prog_num
The value of MYDEF is 4
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--
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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Re: [gmx-users] REMD As A Function of Distance Between 2 Chains
Mark Abraham wrote: Huey Ling Tan wrote: Dear all , thank you for those comments, we are aware of the paper. However, we are not sure how to implement the replica exchange in gromacs. We would like to run a set of replicas in which each replica corresponds to a different set of umbrella parameters. However, when setting up a replica exchange run, all .tpr files use the same .ppa file so that each replica will have the same umbrella potential parameters. Do you know how to get around this problem. You will have to change the code to implement this algorithm.' But first check the pull code in the cvs version of gromacs, where all options have been moved to the mdp file. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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 about energy minimization
renying wrote: Hello, everyone. I have loaded a pdb file of protein complex from Protein Data Bank and put it into water soltion with pdb2gmx, editconf and genbox. After 400 steps of energy minimization when the potential energy seems to be more or less stable, I want to do position restraints. However, it always failed. The error info is as follows: Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.000645 (between atoms 13241 and 13242) rms 0.43 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 13241 13242 31.20.1000 0.0999 0.1000 t = 0.002 ps: Water molecule starting at atom 73326 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates Large VCM(group System): 0.03330, -0.01095, -0.00024, ekin-cm: 2.20013e+03 Check out http://wiki.gromacs.org/index.php/Errors#LINCS_warnings for some ideas. Looking at this water molecule's environment can help. The system seems to be exploding. I have tried the follwing parameters and sadly, none of them works. nsteps = 200/400/800/1000 steps in em.mdp dt = 0.002/0.001/0.0002 ps in pr.mdp tc-grps = Protein SOL or tc-grps = system in pr.mdp tau_t = 0.0020.002 or longer time in pr.mdp If you're sure the problem isn't a water trapped inside a protein or suchlike, one thing you can try is a slow heating. You'll need to do a series of .mdp files with an initial gen_vel to (e.g.) 50K, and then use ref_t to increase that in similar increments. The total charge of the system is -273.000 e and I didn't neutralize it for some reasons. Does this matter much? It probably isn't breaking the numerical simulation, but it could well mean you're not modelling reality. Nature abhors a vacuum, and an isolated charge :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] make gives error in futil.c with mpi and ccc-6.5.6.002-1
I have had some success reproducing the event with a simple c program
and the issue appears to be with the in-house mpicc wrapper script.
The difference between gcc and mpicc appears limited to strings
(-D=\string\) and does not show up in numerical form (e.g. -D=4)
I'll post another update when the issue is resolved.
Chris.
In the following examples cc is the same as mpicc (they both point to
a script called 'compile') but mpicc invokes slightly different
linking options than cc
$ cat prog.c
#include stdlib.h
#include stdio.h
int main(int argn,char *args[]){
printf(The value of MYDEF is %s\n,MYDEF);
}
$ gcc prog.c -DMYDEF=\aaa\ -o prog
$ prog
The value of MYDEF is aaa
$ cc prog.c -DMYDEF=\aaa\ -o prog
cc: Error: prog.c, line 5: In this statement, aaa is not declared.
(undeclared)
printf(The value of MYDEF is %s\n,MYDEF);
--^
###
However, when the defined value is a number, the problem dissapears:
$ cat prog_num.c
#include stdlib.h
#include stdio.h
int main(int argn,char *args[]){
printf(The value of MYDEF is %d\n,MYDEF);
}
$ gcc prog_num.c -DMYDEF=4 -o prog_num
$ prog_num
The value of MYDEF is 4
$ cc prog_num.c -DMYDEF=4 -o prog_num
$ prog_num
The value of MYDEF is 4
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RE: [gmx-users] tabulated bonded interactions
Tabulated bonded interactions will be only in Gromacs 4.0. We should indeed really try to keep the update lists up to date. Berk. From: Ran Friedman [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: [gmx-users] tabulated bonded interactions Date: Wed, 14 Nov 2007 16:33:44 +0100 Dear all, Tabulated bonded interactions have been implemented in December 2006. I wanted to know if they can be used in GMX 3.3.2 or 3.3.3 (and how). I couldn't find a list of changes between 3.3.1 and 3.3.2 online, and even the updates from 3.2 to 3.3 are still under construction according to the web site: http://www.gromacs.org/index.php?option=com_contenttask=categorysectionid=4id=58Itemid=132 Thanks, Ran. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] soft-core and coulomb transformation
Hi, I can see the curves getting overlapped after the code-modification suggested by Berk for ethane to methane coulomb transformations in forward and reverse directions. Thanks Berk and David. bharat On Wed, 14 Nov 2007, bharat v. adkar wrote: hi, even i am also checking the ethane-methane case with the fix you suggested. equilibration values appear to be okay. will let you know by tommorrow the final results.. thanks bharat On Wed, 14 Nov 2007, Berk Hess wrote: Hi, The bug was indeed was I expected. I have fixed it for version 3.3.3. You might not notice it easily, since the direct space contribution is usually larger than the mesh part. But for a two particle system I got nan's. Berk. From: David Mobley [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] soft-core and coulomb transformation Date: Mon, 12 Nov 2007 16:17:36 -0800 Berk, But what do you mean with charging and discharging? Going one way or the other in lambda does not matter. What matters is if there are particles that have zero charge in the A-state topology, while they have a non-zero charge in the B-state topology. Sorry, what I mean by charging versus discharging is that charging is where the A state has zero charges and the B state has normal charges, and discharging is the reverse. So charging is the scenario you describe, and discharging is the reverse. David Berk. From: David Mobley [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: bharat v. adkar [EMAIL PROTECTED] CC: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] soft-core and coulomb transformation Date: Mon, 12 Nov 2007 10:26:37 -0800 Following up on this issue, discharging phenol in water appears to give the same results as charging phenol in water. In other words, so far the only cases for which there seem to be a problem are relative calculations (and so far I haven't looked at this for any other than Bharat's test cases). Bharat, be sure you submit a bugzilla and we'll see how things go from there. I may at some point try setting up some of my own relative free energy topologies and see if I see the same effects, but I'm not likely to have time for that for a couple days. Thanks, David _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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 _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
