Re: [gmx-users] install problem on IBM powerpc AIX 5.3
Hi, thanks for the time I asked my administrator, he told me that there was no mpicc installed on p575, the fore mentioned mpcc was the MPI c compiler, but he is not very familiar with the AIX OS either, and I will try to explain my problem more clearly: a. configure --enable-mpi --prefix=/hpc/gmxmpi I got a error message: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpc b. export MPICC=/usr/bin/mpcc configure --enable-mpi --prefix=/hpc/gmxmpi I got the same error message as (1) c. configure --enable-mpi=/usr/bin/mpcc --prefix=/hpc/gmxmpc the configuration ended without error message, but at the end of the configure output, there was no message telling me that I was compiling with MPI support which usaslly does when I compile it on our Linux Cluster. make mdrun I get the error message: gcc: unrecognized option '-bmaxdata:0x8000 make install-mdrun grompp -f -c -p -o 6np.tpr -sort -shuffle mdrun -v -s 6np.tpr -np 6 -proces 6 -shared_memory then I got the no MPI support error GROMACS compiled without MPI support - can't do parallel runs (4) I checked the Makefile and compared it with the one I successfully compiled on our Linux Cluster, found there was no MPI compiler invoked, for example, the 89th line AS = gcc, 95th line CC = gcc, 96th line CCAS = gcc etc. in fact, this is the first time we try the AIX OS out, we dont even know which is the MPI compiler, maybe the mpcc is not the MPI compiler... I know many of you guys experienced with installation on AIX, any suggestions ? I am totally a newbie... On 10/18/07, Erik Lindahl [EMAIL PROTECTED] wrote: MPICC is the environment variable (upper case important). It should be set to the name of your mpi-enabled C compiler. Cheers, ERik On Oct 18, 2007, at 4:40 AM, liu xin wrote: Hi Erick you mean export MPICC=mpcc? ok, I will try that On 10/18/07, Erik Lindahl [EMAIL PROTECTED] wrote: Hi, On Oct 17, 2007, at 7:13 PM, liu xin wrote: Thanks for your quick comment David but if I tried ./configure --enable-mpi --prefix=/hpc/gromacsmpi it will complain about cant find MPI compiler, but I've already export mpcc=mpicc Try setting MPICC instead :-) Cheers, Erik ___ 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 ___ 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
[gmx-users] Addition of ions in vacuum simulations
Hi all, I am simulating a charged peptide in vacuum. I want to neutralize my system by using genion command,and as expected it asks me a continuous solvent group for the replacement; however, I have no solvents. How can I add ions to my system if I am in vacuum? or Is it necessary to add ions while performing simulations in vacuum? Thanks in advance Ozge ___ 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] install problem on IBM powerpc AIX 5.3
Hi, thanks for the time I asked my administrator, he told me that there was no mpicc installed on p575, the fore mentioned mpcc was the MPI c compiler, but he is not very familiar with the AIX OS either, and I will try to explain my problem more clearly: a. configure --enable-mpi --prefix=/hpc/gmxmpi I got a error message: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpc b. export MPICC=/usr/bin/mpcc configure --enable-mpi --prefix=/hpc/gmxmpi I got the same error message as (1) You need an MPI C compiler. Find out its name. I'd expect b) to work if you use the right name. Otherwise try ./configure --enable-mpi MPICC=name_of_mpi_c_compiler c. configure --enable-mpi=/usr/bin/mpcc --prefix=/hpc/gmxmpc --enable-mpi=/usr/bin/mpcc isn't recognized. Read ./configure --help 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
Re: [gmx-users] Addition of ions in vacuum simulations
Hi all, I am simulating a charged peptide in vacuum. I want to neutralize my system by using genion command,and as expected it asks me a continuous solvent group for the replacement; however, I have no solvents. How can I add ions to my system if I am in vacuum? or Is it necessary to add ions while performing simulations in vacuum? This is a chemistry question that will depend on your protein and what you're trying to study. In some cases you might also consider modifying the chemical groups so that there is not an ion there. 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
Re: Re: [gmx-users] Addition of ions in vacuum simulations
Hi Mark, I think, it is not a chemistry question exactly. Genion command asks for a group whose atoms are replaced with ions. I have no solvent molecules in my system. In this respect, how can I incorporate ions into my system? Thanks Ozge -Original Message- From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thu, 18 Oct 2007 16:49:15 +1000 (EST) Subject: Re: [gmx-users] Addition of ions in vacuum simulations Hi all, I am simulating a charged peptide in vacuum. I want to neutralize my system by using genion command,and as expected it asks me a continuous solvent group for the replacement; however, I have no solvents. How can I add ions to my system if I am in vacuum? or Is it necessary to add ions while performing simulations in vacuum? This is a chemistry question that will depend on your protein and what you're trying to study. In some cases you might also consider modifying the chemical groups so that there is not an ion there. 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 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: Re: [gmx-users] Addition of ions in vacuum simulations
Hi Mark, I think, it is not a chemistry question exactly. Genion command asks for a group whose atoms are replaced with ions. I have no solvent molecules in my system. In this respect, how can I incorporate ions into my system? Check your assumptions. Does it make sense to put isolated ions outside a protein in vacuum? 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
Re: [gmx-users] Addition of ions in vacuum simulations
What Mark means is that there us little meaning of adding ions in a simulation of a protein in vacuum. There is little sense and use of a simulation of a protein in vacuum, but that could depend on what you are looking for. There is little sense in putting ions in a vacuum environment to neutralize your system, this does not depend on your problem. The other option you have to neutralize the system is to neutralize the side-chains so that here is no more net charges in your system. This what is done in a Gromos FF version. check in the pdb2gmx options. XAvier I think, it is not a chemistry question exactly. Genion command asks for a group whose atoms are replaced with ions. I have no solvent molecules in my system. In this respect, how can I incorporate ions into my system? Check your assumptions. Does it make sense to put isolated ions outside a protein in vacuum? 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 - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ 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] qasi-harmonic entropy calculation
Hi all user, I have calculated entroy over time from eigenvalue(g_covar) and the result shows that the entropy decreasing towards zeo. The results is ok as far as it decreases. But I do not understand why it is approaching to zero towards the end of the simulation. Can anyone explain why? I would appreciate your response. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ 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] qasi-harmonic entropy calculation
Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, Pedro. 2007/10/18, Naser, Md Abu [EMAIL PROTECTED]: Hi all user, I have calculated entroy over time from eigenvalue(g_covar) and the result shows that the entropy decreasing towards zeo. The results is ok as far as it decreases. But I do not understand why it is approaching to zero towards the end of the simulation. Can anyone explain why? I would appreciate your response. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ 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
[gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel
Hi This question is about trying to make sure that I am doing the right thing while trying to use tpbconv to restart jobs. After minimization, for the first dynamics run, I use gen_vel = yes. For subsequent restart runs however, gen_vel must be set to no. After the first dynamics run of 200ps, my output is mol-1.edr/trr, and the input for the first dynamics run was mol-1.tpr I can then try to extend the simulation beyond 200 ps using tpbconv with the following options: tpbconv -f mol-1.trr -s mol-1.tpr -e mol-1.edr -extend 200 -o mol-2.tpr The problem with this, however, is that mol-1.tpr was built with gen_vel = yes, which should not be the case when one is restarting the simulation. First question: will this matter at all, because the velocities should be read from the .trr file anyway, and that should overwrite the information in the tpr file ? In order to circumvent the problem, and avoid deshuffling and reshuffling, I wrote another .tpr file for the first dynamics run but with gen_vel set to no. I did not use this tpr file to run the simulation. Lets call this tpr file mol-novelocity-1.tpr. So, the only difference between mol-1.tpr and mol-novelocity-1.tpr is that the former has initialized velocities, while the latter does not. Now, I can use tpbconv to restart the simulation as follows: tpbconv -s mol-1.tpr -f mol-1.trr -e mol-1.edr -extend 200 -o mol-2.tpr I just wanted to confirm if what I am doing makes sense ? Thanks very much for the help ! -Himanshu ___ 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] GROMETA - Gromacs with Metadynamics, and more
Dear Gromacs users, we have developed a GROMACS release with metadynamics. If your are interested in trying it, you can download it from http://lxmi.mi.infn.it/~provasi/grometa/ If you implement new features in it, we'd like to have them included in our version, too, so let us know! Also let us know if you find bugs or errors. Carlo Camilloni and Davide Provasi. Physics deparment, University of Milano via Celoria, 16 20133 Milan, Italy ___ 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] restarting jobs using tpbconv and grompp : with regards to gen_vel
himanshu khandelia wrote: Hi This question is about trying to make sure that I am doing the right thing while trying to use tpbconv to restart jobs. Check out http://wiki.gromacs.org/index.php/Doing_Restarts After minimization, for the first dynamics run, I use gen_vel = yes. For subsequent restart runs however, gen_vel must be set to no. After the first dynamics run of 200ps, my output is mol-1.edr/trr, and the input for the first dynamics run was mol-1.tpr I can then try to extend the simulation beyond 200 ps using tpbconv with the following options: tpbconv -f mol-1.trr -s mol-1.tpr -e mol-1.edr -extend 200 -o mol-2.tpr The problem with this, however, is that mol-1.tpr was built with gen_vel = yes, which should not be the case when one is restarting the simulation. First question: will this matter at all, because the velocities should be read from the .trr file anyway, and that should overwrite the information in the tpr file ? gen_vel is only used by grompp In order to circumvent the problem, and avoid deshuffling and reshuffling, I wrote another .tpr file for the first dynamics run but with gen_vel set to no. I did not use this tpr file to run the simulation. Lets call this tpr file mol-novelocity-1.tpr. So, the only difference between mol-1.tpr and mol-novelocity-1.tpr is that the former has initialized velocities, while the latter does not. Now, I can use tpbconv to restart the simulation as follows: tpbconv -s mol-1.tpr -f mol-1.trr -e mol-1.edr -extend 200 -o mol-2.tpr I just wanted to confirm if what I am doing makes sense ? Thanks very much for the help ! These two output .tpr files should be the same except for the initial steps and times, unless your mol-2.mdp file took care of that. You can use gmxcheck to test for the differences. ___ 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] restarting jobs using tpbconv and grompp : with regards to gen_vel
This question is about trying to make sure that I am doing the right thing while trying to use tpbconv to restart jobs. After minimization, for the first dynamics run, I use gen_vel = yes. For subsequent restart runs however, gen_vel must be set to no. After the first dynamics run of 200ps, my output is mol-1.edr/trr, and the input for the first dynamics run was mol-1.tpr I can then try to extend the simulation beyond 200 ps using tpbconv with the following options: tpbconv -f mol-1.trr -s mol-1.tpr -e mol-1.edr -extend 200 -o mol-2.tpr This is correct. tpbconv will take the velocities in the mol-1.tpr The problem with this, however, is that mol-1.tpr was built with gen_vel = yes, which should not be the case when one is restarting the simulation. First question: will this matter at all, because the velocities should be read from the .trr file anyway, and that should overwrite the information in the tpr file ? In order to circumvent the problem, and avoid deshuffling and reshuffling, I wrote another .tpr file for the first dynamics run but with gen_vel set to no. I did not use this tpr file to run the simulation. Lets call this tpr file mol-novelocity-1.tpr. So, the only difference between mol-1.tpr and mol-novelocity-1.tpr is that the former has initialized velocities, while the latter does not. Good trial but this will not work! It is not possible to have a tpr file without velocities. If you set gen_v to no and do not give a gro/tpr/trr file for it to read the velocities it will generate new ones anyways. Now, I can use tpbconv to restart the simulation as follows: tpbconv -s mol-1.tpr -f mol-1.trr -e mol-1.edr -extend 200 -o mol-2.tpr I just wanted to confirm if what I am doing makes sense ? Thanks very much for the help ! -Himanshu - XAvier Periole - PhD - Institute of Molecular Assemblies City University of New York - USA - Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ 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] restarting jobs using tpbconv and grompp : with regards to gen_vel
Check out http://wiki.gromacs.org/index.php/Doing_Restarts Thanks very much. I do understand the general restarting mechanism. It is only the first restart that was a little bit confusing I just wanted to confirm if what I am doing makes sense ? Thanks very much for the help ! These two output .tpr files should be the same except for the initial steps and times, unless your mol-2.mdp file took care of that. You can use gmxcheck to test for the differences. Sorry I did not understand ? There is no mol-2.mdp file. So, in effect the first tpbconf command should work. The velocities will be obtained from the .trr file and not the .tpr file, correct ? That is the main issue bothering me, because the .tpr file contains the initial velocities generated during the first run. tpbconv -f mol-1.trr -s mol-1.tpr -e mol-1.edr -extend 200 -o mol-2.tpr Thanks again, -himanshu ___ 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] qasi-harmonic entropy calculation
Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote: Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, The CVS head version of g_anaeig computes these values as well. -- 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] qasi-harmonic entropy calculation
Hi Pedro, Thank you for your attention to my email. Yes, I am using Schlitter equation and the rusult is cumulative. The entropy is meant to be decreased as the protein is stick on to a surface. I have used the entire protein as a subset. Is the programme takes the final structure for calculating covariance? With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Pedro Alexandre de Araújo Gomes Lapido Loureiro Sent: Thu 18/10/2007 1:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] qasi-harmonic entropy calculation Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, Pedro. 2007/10/18, Naser, Md Abu [EMAIL PROTECTED]: Hi all user, I have calculated entroy over time from eigenvalue(g_covar) and the result shows that the entropy decreasing towards zeo. The results is ok as far as it decreases. But I do not understand why it is approaching to zero towards the end of the simulation. Can anyone explain why? I would appreciate your response. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ 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
RE: [gmx-users] qasi-harmonic entropy calculation
Hi David, Thanks for your information and I will have a look CVS head version. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Thu 18/10/2007 4:18 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] qasi-harmonic entropy calculation Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote: Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, The CVS head version of g_anaeig computes these values as well. -- 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 ___ 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] qasi-harmonic entropy calculation
Maybe there has been some mistake during your calculations? No, g_covar gives the average covariance matrix. You can check this matrix with the command -ascii. If you have used your own program to calculate entropy double check units conversion stuff. Regards. Pedro. 2007/10/18, Naser, Md Abu [EMAIL PROTECTED]: Hi Pedro, Thank you for your attention to my email. Yes, I am using Schlitter equation and the rusult is cumulative. The entropy is meant to be decreased as the protein is stick on to a surface. I have used the entire protein as a subset. Is the programme takes the final structure for calculating covariance? With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Pedro Alexandre de Araújo Gomes Lapido Loureiro Sent: Thu 18/10/2007 1:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] qasi-harmonic entropy calculation Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, Pedro. 2007/10/18, Naser, Md Abu [EMAIL PROTECTED]: Hi all user, I have calculated entroy over time from eigenvalue(g_covar) and the result shows that the entropy decreasing towards zeo. The results is ok as far as it decreases. But I do not understand why it is approaching to zero towards the end of the simulation. Can anyone explain why? I would appreciate your response. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ 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 ___ 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] install problem on IBM powerpc AIX 5.3
Hi Mark After some search on the web, I found that in AIX OS mpcc is the MPI c compiler, while mpCC is the MPI C++ compiler and mpxlf is the MPI fortran compiler. but when I tried to configure it like: configure --enable-mpi MPICC=/usr/bin/mpcc, I still got error complaining Cannot compile and link MPI code with mpcc. On 10/18/07, Mark Abraham [EMAIL PROTECTED] wrote: Hi, thanks for the time I asked my administrator, he told me that there was no mpicc installed on p575, the fore mentioned mpcc was the MPI c compiler, but he is not very familiar with the AIX OS either, and I will try to explain my problem more clearly: a. configure --enable-mpi --prefix=/hpc/gmxmpi I got a error message: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpc b. export MPICC=/usr/bin/mpcc configure --enable-mpi --prefix=/hpc/gmxmpi I got the same error message as (1) You need an MPI C compiler. Find out its name. I'd expect b) to work if you use the right name. Otherwise try ./configure --enable-mpi MPICC=name_of_mpi_c_compiler c. configure --enable-mpi=/usr/bin/mpcc --prefix=/hpc/gmxmpc --enable-mpi=/usr/bin/mpcc isn't recognized. Read ./configure --help 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 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] install problem on IBM powerpc AIX 5.3
Mark Abraham wrote: liu xin wrote: Hi Mark After some search on the web, I found that in AIX OS mpcc is the MPI c compiler, while mpCC is the MPI C++ compiler and mpxlf is the MPI fortran compiler. but when I tried to configure it like: configure --enable-mpi MPICC=/usr/bin/mpcc, I still got error complaining Cannot compile and link MPI code with mpcc. Well, look at the last few hundred lines of config.log and see what you find by the way of error messages when configure tries to use mpcc to compile and link. You should also use ./configure to make sure that you are running the configure in the gromacs install directory, not some other configure in your path. 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
