[gmx-users] density map in 3 Dimension
Dear gromacs-users, I thought of sending this query again as I did not get any response in my last email. I was wondering whether there is any way to calculate the 3D density map of a particular selection of protein-water system ( say the water near the protein backbone) in gromacs. I guess g_densmap provides a 2D map of the density. But I was looking for 3D map of density. I presume it might have to do with calculating volume of a space. But, I am not sure how to do it in gromacs. Any help will be appreciated. Jagannath-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] 3D density Map
Dear Gromacs users, I was wondering whether there is any way to calculate the 3D density map of a particular selection of protein-water system ( say the water near the protein backbone) in gromacs. I guess g_densmap provides a 2D map of the density. But I was looking for 3D map of density. I presume it might have to do with calculating volume of a space. But, I am not sure how to do it in gromacs. Any help will be appreciated. Jagannath-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem with replica exchange
Hi, I am having a problem in running replica exchange simulation over multiple nodes. To run the simulation for 16 replicas over two 8-core processors, I generated a hostfile as follows: yethiraj30 slots=8 max_slots=8 yethiraj31 slots=8 max_slots=8 These two machines are intra-connected and I have installed openmpi Then If I try to run the replica exchange simulation using the following command:mpirun -np 16 --hostfile hostfile mdrun_4mpi -s topol_.tpr -multi 16 -replex 100 log_replica_test But I find following error and mdrun does not proceed at all : NNODES=16, MYRANK=0, HOSTNAME=yethiraj30NNODES=16, MYRANK=1, HOSTNAME=yethiraj30NNODES=16, MYRANK=4, HOSTNAME=yethiraj30NNODES=16, MYRANK=2, HOSTNAME=yethiraj30NNODES=16, MYRANK=6, HOSTNAME=yethiraj30NNODES=16, MYRANK=3, HOSTNAME=yethiraj30NNODES=16, MYRANK=5, HOSTNAME=yethiraj30NNODES=16, MYRANK=7, HOSTNAME=yethiraj30[yethiraj30][[22604,1],0][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113)[yethiraj30][[22604,1],4][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113)[yethiraj30][[22604,1],6][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113)[yethiraj30][[22604,1],1][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113)[yethiraj30][[22604,1],3][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113)[yethiraj30][[22604,1],2][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113)NNODES=16, MYRANK=10, HOSTNAME=yethiraj31NNODES=16, MYRANK=12, HOSTNAME=yethiraj31 I am not sure how to resolve this issue. In general, I can go from one machine to another without any problem using ssh. But, when I am trying to run openmpi over both the machines, I get this error. Any help will be appreciated. Jagannath -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with energy groups and mdrun -rerun option
Justin,Thanks for your reply. Then I wonder whether there is any other way out in gromacs to get the net interaction potential energy due to each of the components in a simulations. I am asking this, many times people report the potential energy contribution due to solvent-solvent interaction in a simulation containing solute( say peptide) and solvents and that are also being done in gromacs. I wonder, for those cases, whether just adding the non-bonding interaction will be good enough ? or, there is any other way out ?Jagannath --- On Fri, 22/10/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] problem with energy groups and mdrun -rerun option To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 22 October, 2010, 2:56 AM jagannath mondal wrote: Hi, I have used gromacs 4.0.7 to do MD simulation of two solutes A B in water ( solvent) . Initially, I had set energy groups = system and used mdrun to do the simulation. Now,I wanted to get the potential energy contribution from due to interaction of A-A, B-B,A-B A-solvent, B-solvent, solvent-solvent. For that I followed some discussions in mailing list regarding using mdrun -rerun option: This is what I did: I used make_ndx and created 3 groups: A, B and solvent. Now, I modified the grompp.mdp file so that I have now energy groups = A B solvent Then I used grompp -c conf -f grompp -n index -o topol Then I used mdrun -s -rerun traj_old.xtc ( here traj_old.xtc is the old xtc file I obtained during the original mdrun) But, now, after using this -rerun option , if I try to use the g_energy on the resulting ener.edr file to obtain the individual potential energy of interaction for A-A, B-B , A-B, A-solvent I get following output Here is the output from g_energy -f ener.edr : Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. --- 1 Bond 2 Angle 3 U-B 4 Ryckaert-Bell. 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR) 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Kinetic-En. 13 Total-Energy 14 Conserved-En. 15 Temperature 16 Pressure-(bar) 17 Cons.-rmsd-() 18 Vir-XX 19 Vir-XY 20 Vir-XZ 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX-(bar) 28 Pres-XY-(bar) 29 Pres-XZ-(bar) 30 Pres-YX-(bar) 31 Pres-YY-(bar) 32 Pres-YZ-(bar) 33 Pres-ZX-(bar) 34 Pres-ZY-(bar) 35 Pres-ZZ-(bar) 36 #Surf*SurfTen 37 Mu-X 38 Mu-Y 39 Mu-Z 40 Coul-SR:A-A 41 LJ-SR:A-A 42 Coul-14:A-A 43 LJ-14:A-A 44 Coul-SR:A-B 45 LJ-SR:A-B 46 Coul-14:A-B 47 LJ-14:A-B 48 Coul-SR:A-Solvent 49 LJ-SR:A-Solvent 50 Coul-14:A-Solvent 51 LJ-14:A-Solvent 52 Coul-SR:B-B 53 LJ-SR:B-B 54 Coul-14:B-B 55 LJ-14:B-B 56 Coul-SR:B-Solvent 57 LJ-SR:B-Solvent 58 Coul-14:B-Solvent 59 LJ-14:B-Solvent 60 Coul-SR:Solvent-Solvent 61 LJ-SR:Solvent-Solvent 62 Coul-14:Solvent-Solvent 63 LJ-14:Solvent-Solvent 64 T-System 65 Xi-System It provides me contribution from each of the energy groups on nonbonding terms: LJ(SR),Coulomb(SR),Coulomb(14),LJ(14) . But, it does NOT provide me their contribution to Bonding term( i.e bond,angle, U-B,RB,improper-Dih) !! As a result, I am a not sure how to get the net potential energy from each of the 3 energy groups. Am I doing something wrong ? Do I need to use any other utilities ? Using energygrps only allows you to decompose nonbonded interactions. You cannot decompose bonded interactions, potential, kinetic energy, etc. -Justin Any help will be useful. Jagannath -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests
[gmx-users] molecular surface area(MSA)?
Hi, I was wondering whether gromacs can calculate a quantity called molecular surface area(MSA) which is different from solvent accessible surface area(SASA). By definition, SASA of a molecule is the area of surface traced by center of a spherical water probe rolling on a vander wall surface of the given molecule. I think g_sas provides SASA. But MSA is something different. It is the area generated by the part of the probe surface facing the given molecule. But, I am not sure whether gromacs can calculate it . Jagannath -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem with trjconv -pbc cluster
Hi, I had a system of surfectants which are started with an initial configuration where all of them are well dispersed. Visual study of trajectory shows they start aggregating and finally form two discrete micelles. To quantify this micelle clusterization, I tried to use the suggestions present in the gromacs documentations: http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering i.euse trjconv -pbc cluster to obtain a single frame that has all of the lipids in the unit cell. This must be the first frame of your trajectory. A similar frame from some previous timepoint will not work.use grompp to make a new tpr file based on the frame that was output from the step above.use trjconv -pbc nojump to produce the desired trajectory using the newly produced tpr file.trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc clustergrompp -f a.mdp -c a_cluster.gro -o a_cluster.tprtrjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump But, The first step i.e. trjconv -pbc cluster does not work. Looks like it is going through an infinite loop and is not stopping for convergence. I am using gromacs 4.0.7 Any help will be appreciated. Jagannath -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with trjconv -pbc cluster
Thanks for the reply. I used following command to extract first frame that has all the surfectants ( as suggested by first step for characterizing micelle clustering). trjconv -f a.xtc -o a_cluster.gro -dump 0 -pbc cluster Here is the output I got:COM: 0.000 0.000 19.999 iter = 19526 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19527 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19528 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19529 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19530 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19531 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19532 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19533 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19534 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19535 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19536 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19537 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19538 Isq = 12671033.000 looks like lsq is only fluctuating between two numbers and the program is in an infinte loop. Jagannath --- On Wed, 7/7/10, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] problem with trjconv -pbc cluster To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, 7 July, 2010, 12:20 PM - Original Message - From: jagannath mondal jmondal2...@yahoo.co.in Date: Wednesday, July 7, 2010 16:36 Subject: [gmx-users] problem with trjconv -pbc cluster To: gmx-users@gromacs.org Hi, I had a system of surfectants which are started with an initial configuration where all of them are well dispersed. Visual study of trajectory shows they start aggregating and finally form two discrete micelles. To quantify this micelle clusterization, I tried to use the suggestions present in the gromacs documentations: http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering i.e use trjconv -pbc cluster to obtain a single frame that has all of the lipids in the unit cell. This must be the first frame of your trajectory. A similar frame from some previous timepoint will not work. use grompp to make a new tpr file based on the frame that was output from the step above. use trjconv -pbc nojump to produce the desired trajectory using the newly produced tpr file. trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump But, The first step i.e. trjconv -pbc cluster does not work. Looks like it is going through an infinite loop and is not stopping for convergence. So what command did you give, what output did you get, and does the command make sense with respect to your trajectory contents? Mark I am using gromacs 4.0.7 Any help will be appreciated. Jagannath -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with trjconv -pbc cluster
Hi Chris, Thanks a lot for your responses. I will surely try them. But, before I go to trjconv -pbc cluster, I had one more problem to sort out. This has to do with quantifying the cluster-size distribution from the trajectory. As I mentioned, if I visualize the trajectory in VMD, I see that starting from a random dispersed state of 50 molecules of surfactant, it aggregates gradually and at a long time, two distinct miceller aggregates are formed.But, If I try to quantify the cluster-size distribution using g_clustsize utilty, it gives me bizarre results: the maxclust.xvg for the final time frame shows that I have 1 single cluster containing all the 50 molecules. But, Vmd shows 2 distinct aggregate. Here is the command line I used: g_clustsize -f traj.xtc -s topol -mol -cut 0.50 I used -mol option so that I get the cluster size distribution in terms of the molecules.Here, executing the commands gives me maxclust.xvg which has maximum size of clusters( in terms of molecule number) as a function of time frame. It shows at the end, maxclustersize is 50 and it has all the particles in it( as obtained from maxclust.ndx)Besides, at any other time, the maximum size of particles predicted by g_clustsize does not match with what VMD shows. I also tried post-processing the trajectory using trjconv with -pbc whole or with -pbc nojump . But, g_clustsize always returns same result:maxcluster contains all the particles.Then I tried playing with -cut option : I started with default value of 0.35, here the result is worse: it shows maxclust = 1 i.e all the particles are monomeric . But any value beyond 0.35 gives me maxclust = 50. I tried to cross-check whether visualization is misrepresented or not: for this I tried to calculate all the distances among the com of the surfectants using g_dist tool and tried to manually cluster the surfectants and I found that here I can easily come up with two separate cluster based on the distances. So, I think that the problem lies in g_clustsize not in visualization, as -pbc whole or -pbc nojump does not change the result.So, do you have any suggestions ? Any help in pointing out where I am doing wrong will be helpful.Jagannath --- On Wed, 7/7/10, chris.ne...@utoronto.ca chris.ne...@utoronto.ca wrote: From: chris.ne...@utoronto.ca chris.ne...@utoronto.ca Subject: [gmx-users] problem with trjconv -pbc cluster To: gmx-users@gromacs.org Date: Wednesday, 7 July, 2010, 9:27 PM PS: you realize that trjconv -pbc cluster is never going to work unless you actually have a cluster, right? So you can't start this procedure near your initial dispersed state. You need to start at some time T where you actually do have a cluster. Then you can try -dump T, -dump (T+X), -dump (T+X*2), etc. Then you can follow the ides expressed below like running backwards with -pbc nojup to get the initial state. Chris. --original message -- Dear Jagannath: There is, as far as I know, no way to fix this. Here's what you should do. 1. Let the space between your timesteps be X ps. 2. Use trjconv -pbc cluster -dump X -o out.gro 2b. if that doesn't work, try trjconv -pbc cluster -dump (X*2) -o out.gro 2c. if that doesn't work, try trjconv -pbc cluster -dump (X*3) -o out.gro ... (Note use real numbers for args to -dump). Once you have a frame that works, you can run part 2 and 3 of that wiki page by making a tpr based on the gro that worked -- and I think that you'll need to run your trjconv -pbc mol starting from the frame where clustering worked (e.g. -b X). Note that this second requirement means that you may need to reverse the frames from your .xtc file so that you can run in reverse time from a complete micelle through to disassembly with -pbc nojump -- a for loop around trjconv will work but inefficiently, you might be able to use -demux smartly here (I'm not sure). But then since you have 2 micelles you will need a starting box in which they are both whole getting trickier. You should be aware that the trjconv -pbc cluster is not the only way to do part 1 from that wiki page. You could use trjconv -trans X Y Z and then make a new .tpr and then run trjconv -pbc nojump and it would work if only you knew which X Y Z to use (although trial and error may help you here eventually). Sorry this is confusing, but this is a difficult thing to do and you should expect to struggle with it for some time, so another questino to ask yourself is do I really need to do this? If its just for making a movie then you can use pbctools in vmd for that. Chris. -- original message -- Hi, I had a system of surfectants which are started with an initial configuration where all of them are well dispersed. Visual study of trajectory shows they start aggregating and finally form two discrete micelles. To quantify this micelle clusterization, I tried to use the suggestions present in the gromacs documentations: http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering i.e use
Re: [gmx-users] problem with g_clustsize
Thanks. Just wondering what is a 'distal atom' as you mentioned. I am creating a new subject on g_clustsize. --- On Wed, 7/7/10, chris.ne...@utoronto.ca chris.ne...@utoronto.ca wrote: From: chris.ne...@utoronto.ca chris.ne...@utoronto.ca Subject: [gmx-users] problem with trjconv -pbc cluster To: gmx-users@gromacs.org Date: Wednesday, 7 July, 2010, 10:26 PM I wrote my own program to do this and so I never tried that one. We did find that clustering based on a dingle atom in the chain was a very good idea. So take your distal carbon in the surfactant and make in index group of it and cluster it (with a larger cutoff) with g_clustsize. Obviously if there is a problem with g_clustsize then you should also file a bugzilla. If you're going to continue with this thread about g_clustsize, then please pick an appropriate subject line so that others can search it usefully later. Chris. -- original message -- Hi Chris, Thanks a lot for your responses. I will surely try them. But, before I go to trjconv -pbc cluster, I had one more problem to sort out. This has to do with quantifying the cluster-size distribution from the trajectory. As I mentioned, if I visualize the trajectory in VMD, I see that starting from a random dispersed state of 50 molecules of surfactant, it aggregates gradually and at a long time, two distinct miceller aggregates are formed.But, If I try to quantify the cluster-size distribution using g_clustsize utilty, it gives me bizarre results: the maxclust.xvg for the final time frame shows that I have 1 single cluster containing all the 50 molecules. But, Vmd shows 2 distinct aggregate. Here is the command line I used: g_clustsize -f traj.xtc -s topol -mol -cut 0.50 I used -mol option so that I get the cluster size distribution in terms of the molecules.Here, executing the commands gives me maxclust.xvg which has maximum size of clusters( in terms of molecule number) as a function of time frame. It shows at the end, maxclustersize is 50 and it has all the particles in it( as obtained from maxclust.ndx)Besides, at any other time, the maximum size of particles predicted by g_clustsize does not match with what VMD shows. I also tried post-processing the trajectory using trjconv with -pbc whole or with -pbc nojump . But, g_clustsize always returns same result:maxcluster contains all the particles.Then I tried playing with -cut option : I started with default value of 0.35, here the result is worse: it shows maxclust = 1 i.e all the particles are monomeric . But any value beyond 0.35 gives me maxclust = 50. I tried to cross-check whether visualization is misrepresented or not: for this I tried to calculate all the distances among the com of the surfectants using g_dist tool and tried to manually cluster the surfectants and I found that here I can easily come up with two separate cluster based on the distances. So, I think that the problem lies in g_clustsize not in visualization, as -pbc whole or -pbc nojump does not change the result.So, do you have any suggestions ? Any help in pointing out where I am doing wrong will be helpful.Jagannath --- On Wed, 7/7/10, chris.neale at utoronto.ca chris.neale at utoronto.ca wrote: From: chris.neale at utoronto.ca chris.neale at utoronto.ca Subject: [gmx-users] problem with trjconv -pbc cluster To: gmx-users at gromacs.org Date: Wednesday, 7 July, 2010, 9:27 PM -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] fftw library problem in gromacs installation
Hi , I am having a problem in installing gromacs-4 in a suse linux in a powerpc ibm machine. The problem is that 1. I first installed fftw in the following way :for single precision./configure --enable-float --enable-threads --prefix=/N/u/tg-jmondal/BigRed/UTIL/fftwmakemake install Then for double precisionmake distclean./configure --enable-threads --prefix=/N/u/tg-jmondal/BigRed/UTIL/fftwmakemake install 2. It installed both of them : 3. Now, when I tried to install gromacs4 ./configure --prefix=/N/u/tg-jmondal/BigRed/UTIL/gromacs_mod_4_gcc/ --enable-mpi --program-suffix=mod_4mpi CPPFLAGS=-I/N/u/tg-jmondal/BigRed/UTIL/fftw/include LDFLAGS=-L/N/u/tg-jmondal/BigRed/UTIL/fftw/lib --without-x Here the mpi version is openmpi I get following error:configure: error: Cannot find fftw3f libraryBut, as you may see I have specified the fftw library in configure script So, I went inside config.log file and found the following error: mpicc -o conftest -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -maltivec -mabi=altivec -std=gnu99 -mcpu=7450 -mtune=970 -I/N/u/tg-jmondal/BigRed/UTIL/fftw/include -maltivec -mabi=altivec -L/N/u/tg-jmondal/BigRed/UTIL/fftw/lib conftest.c -lfftw3f -lm 5/usr/bin/ld: skipping incompatible /N/u/tg-jmondal/BigRed/UTIL/fftw/lib/libfftw3f.a when searching for -lfftw3f/usr/bin/ld: cannot find -lfftw3f Looks like there is an incompatibility of mpicc with the fftw library and it may cause some problem. But , I do not know how to resolve this incompatibiilty. Any help will be really appreciated .ThanksJagannath -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_angle between center of mass of three groups
Thanks, But I guess the g_angle -ov option will give me an average angle for many different groups. That will not be same as the angle between center of masses of different group . For example If I have a molecule CH3-CH2-CH3, g_angle -ov can give me an average over angle H-C-H and C-C-C . But what I want is the angle CH3-CH2-CH3 . So, I was wondering whether you can clarify a bit on how I can get it. Thanks Jagannath --- On Wed, 4/11/09, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] g_angle between center of mass of three groups To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, 4 November, 2009, 9:00 AM jagannath mondal wrote: Hi, I know that g_dist gives the distance between the center of masses of two groups. But, I wanted to know whether it is possible to calculate angle between center of masses of three groups or not . I am not sure whether g_angle can calculate the angle between center of masses of three groups. If not, In that case, can anyone suggest suggest any other alternative ? You should start by reading g_angle -h and g_sgangle -h. g_angle will calculate the average over a group of angles, which is similar to what you want. Mark ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php From cricket scores to your friends. Try the Yahoo! India Homepage! http://in.yahoo.com/trynew___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_angle between center of mass of three groups
Hi, I know that g_dist gives the distance between the center of masses of two groups. But, I wanted to know whether it is possible to calculate angle between center of masses of three groups or not . I am not sure whether g_angle can calculate the angle between center of masses of three groups. If not, In that case, can anyone suggest suggest any other alternative ? Jagannath Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to get centre of mass bond angle distribution
Hi, I am trying to coarse-grain a system. For that I want to optimize the bond , angle and dihedral parameters of coarse-grained model based on atomistic simulation. For that, in the atomistic simulation part, I want to calculate the the distribution of 'effective' angle made by the 'centre of mass' of the atoms used for coarse-graining ( in stead of using one of the representative atoms used for coarse-graining ). For example, if I have a molecule H3C-CH2-CH3, I want to calculate the angle-distribution of H3C-CH2-CH3 in stead of C-C-C and bond-distribution of H3C-CH2 in stead of C-C . But I do not know how can I invoke the centre of mass of a group of atoms in the index file for g_angle or g_bond. Do I need to create some dummy atoms? If so, how can I do that? Any help will be highly appreciated. Thanks Jagannath Keep up with people you care about with Yahoo! India Mail. Learn how. http://in.overview.mail.yahoo.com/connectmore___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] comparison of gromacs in CENTOS and UBUNTU
Hi, I was planning to install one of the linux distributions : CENTOS or UBUNTU in our xeon 8-core processor. Can any one suggest which one will be better for Gromacs as far as installation and performance is concerned?ThanksJagannath Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs-3.3.1 tpr file in gromacs 4.0.5?
Hi, I was wondering whether one can use a .tpr file made using gromacs-3.3.1 in gromacs 4.0.5 to restart or exactly continue a simulation or not.ThanksJagannath Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with mpi
Hi,I am trying to use parallel gromacs3.3.3 mdrun programme .I have installed mpich2 in our quadcore machine. But I am having 3 problems: 1. The scaling is very poor among 4 cores: varies between 30-70 %. 2. If I run the mdrun_mpi in background, the output log file cites following error: mpiexec_yethiraj22 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null3. The simulation also crashed citing error in the output log file: *** glibc detected *** mdrun_mpi: malloc(): memory corruption (fast): 0x0c37ea90 ***. Any help and suggestion in this regard will be highly appreciated.ThanksJagannath Mondal Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition http://downloads.yahoo.com/in/firefox/?fr=om_email_firefox___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mpi problem
Hi,I am trying to use parallel gromacs3.3.3 mdrun programme .I have installed mpich2 in our quadcore machine. But I am having 3 problems: 1. The scaling is very poor among 4 cores: varies between 30-70 %. 2. If I run the mdrun_mpi in background, the output log file cites following error: mpiexec_yethiraj22 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null3. The simulation also crashed citing error in the output log file: *** glibc detected *** mdrun_mpi: malloc(): memory corruption (fast): 0x0c37ea90 ***. Any help and suggestion in this regard will be highly appreciated.ThanksJagannath Mondal Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition http://downloads.yahoo.com/in/firefox/?fr=om_email_firefox___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] implicit solvent in gromacs 4.0?
Hi, I was curious to know whether gromacs 4.0 supports implicit solvent simulation or not. If not, is there any possibility that the implicit solvent model will be implemented in near future ? Thanks Jagannath Mondal Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.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] problem with structure factor in g_rdf
Hi, I was trying to use g_rdf analysis tool to calculate the structure factor of a polymer I am simulating. I have generated own ..itp files for the polymer and the simulation is going ok. But, whenever, I am trying to use g_rdf tool to calculate the structure factor, it returns the following error: Reading frames from gro file '', 89600 atoms. Reading frame 0 time0.000 --- Program g_rdf, VERSION 3.3.1 Source code file: gmx_rdf.c, line: 819 Fatal error: Error: atom type (NH3) not in list (18 types checked)! The command line I am using is as follows: g_rdf -f conf.gro -n index.ndx -o rdf2.xvg -sq sq.xvg -s topol.tpr If I only try to calculate the rdf, it goes fine. But only when I am using -sq option , I am getting the error. I checked with gromacs mailing list and I saw an email having similar problem as mine but I did not find any solution. It will be great, if any one can help me with this problem. Thanks Jagannath Download prohibited? No problem. CHAT from any browser, without download. Go to http://in.messenger.yahoo.com/webmessengerpromo.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] request for help to prepare a 111 gold surface
Hi, I am trying to start a simulation involving self-assembly of protein on Au (111) surface where 111 designates the miller indices of the plane. I know how to construct a FCC lattice and the coordinates of a system using Fortran code. But I have no clue of how to get the coordinates of (111) plane of FCC lattice (possibly by modifying the Fortran code for FCC lattice construction). When I searched similar kind of work on gromacs user archive I found plenty of discussions regarding the simulation of this kind . However,Though It may be trivial for most simulation-people, I did not get any idea (mainly technical details) of how to get the coordinates of a (111) surface. Any help in this respect (regarding algorithm of constructing 111 surface or corresponding Fortran code ) will be greatly appreciated. Also, let me know whether there is any option in gromacs or any other programme to generate the 111 surface. . Thanks in advance, Jagannath Mondal Download prohibited? No problem! To chat from any browser without download, Click Here: http://in.messenger.yahoo.com/webmessengerpromo.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] problem with freeze-group : Large VCM(Berk Hess)
Hi Berk, Thanks a lot for your reply. According to your suggestion, I did not remove the cmm for the WHOLE molecule i.e I used 'cmm-mode=None'for the entire system. (Did you mean that I should have removed the restriction only for freeze-group or for whole system?) But now I have two problems: 1) the simulation is now going for longer time but finally again crashes. 2) I freezed the mainchain because I did not want the mainchain move at all and I wanted the only side-chain move. But , when I am visualising the trajectory in VMD, I am finding that whole molecule is tumbling including the main-chain i.e the whole molecule is changing its position. As ususal, I did not use pressure coupling . Do you think that the movement of whole molecule is expected during freeze group simulation? should I modify something else in my parameter file? I am again giving the .mdp file. --- Berk Hess [EMAIL PROTECTED] wrote: From: jagannath mondal [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] problem with freeze-group : Large VCM Date: Fri, 11 May 2007 00:19:53 +0100 (BST) Hi Gromacs user, I am a gromacs beginner struggling with freeze-group simulation. I was trying to simulate a beta-peptide(un-natural peptide ) by relaxing only the side-chains but I am getting error regarding large VCM and The system has only 1 peptide (14-residue ) and No solvent. So, for this purpose , I generated a freeze-group which contains all the main-chain atoms. Initially I was using pressure-coupling and it was giving error in simulation. Later I found many discussion on this freeze-group simulation in user-archive and manual and accordingly I did not use pressure-coupling in my simulation and before the simulation, I minimised my peptide using steep integrator and then with the minimised structure I tried a MD run. But after 40 ps, the mdrun crashes with complaint about nsgrid and large VCM: You should not remove com motion when using freeze groups, since the com is no longer free to move. We should let grompp print a warning for this. Berk. _ 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 Office firewalls, cyber cafes, college labs, don't allow you to download CHAT? Click here: http://in.messenger.yahoo.com/webmessengerpromo.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] query regarding a topology file
Hi, I am trying to prepare a gromacs topology file for a non-natural peptide. For that I prepared a molecule.itp file and a corresponding ff***bon.itp file which contains all the bond-type, angle-type and dihedral-type. But, when I try to use grompp for generating the .tpr file, it shows the following statement (But these are not 'warnings') . The following terms are atom indices and they are implying RB dihedrals. Skip RB 204 206 208 209 (zero contribution) Skip RB 207 206 208 209 (zero contribution) Skip RB 207 206 208 210 (zero contribution) Skip RB 207 206 208 213 (zero contribution) skip RB 211 210 229 230(zero contribution) But the corresponding dihedral types are present in the ff**bon.itp file.(For example 211 210 229 230 implies HB CT2 C O), But still why is it skipping those dihedrals ? previously, if it could not find any dihedral type it used to give an warning for not showing that, But In this case, it is skipping some dihedral types though they are present in the ff***bon.itp file. Can you say whether this is a serious error or it is OK? Thanks, Jagannath Mondal ___ gmx-users mailing list[EMAIL PROTECTED] 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] what are the options for implicit solvent in Gromacs?
Hi, I am trying to learn how to use implicit solvent model for PMF calculation. For that ,I wanted to know what are the options for implicit solvent present in gromacs. But I could not find any documentation regarding that. I searched mailing list and found that there has been some query on the documentation but I could not find any suitable reply. In one of the reply, David suggested using following command: touch grompp grompp But it does not show all the available option for implicit solvent model gromacs has got. it shows implicit solvent= no. There were some older mail (before 2006) where it was said that gromacs has not gor implicit solvent model. But I hope that latest version has got implicit solvent model. Can anyone suggest any documentation where I can find the availble options for implicit solvent model as well as the other options for Generalized Born model? Thanks in advance,, Yours sincerely, Jagannath Mondal ___ gmx-users mailing list[EMAIL PROTECTED] 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] query regarding a topology file
Thanks for reply. Yes, it uses the force-field file I created. Basically I found out that the dihedral which the program skips is also 0. On Apr 12, 2007, at 8:43 PM, Dallas B. Warren wrote: Can't really help you directly, but it comes to mind when I read that error that may be something is incorrectly defined or formatted within your files. It is not picking up the actual values, or something like that? Is it using the forcefield files you created? Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing list[EMAIL PROTECTED] 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 list[EMAIL PROTECTED] 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] query regarding topology file
Hi, I am a gromacs beginner. I am trying to simulate a non natural peptide. I have prepared a standalone molecule .itp file for my molecule and I have prepared a corresponding topology file (topol.top) which include the .itp file. Now, I used the genconf option to replicate my molecule of my interest so that I can get 2 molecules . The genconf program gives rise to gro file in which all of the atoms has got 0 velocity. Can anyone suggest what I should do to get a random velocity for each of the atoms in my initial gro file or is it ok even if all the atoms has got 0 initial velocity and during simulation it gains a random velocity ? Yours sincerely Jagannath Mondal ___ 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] Query regarding PDB2gmx
HI, I am a gromacs beginner. I am trying to simulate a non natural peptide. I have prepared a standalone molecule .itp file for my molecule and I have prepared a corresponding topology file (topol.top) which include the .itp file. First, I was trying to get a .gro file from the PDB file of my molecule. But, when-ever I try to use the pdb2gmx command it always ask to choose amongthe shared topologies present in gromacs library in stead of refering to my own topology file present in working directory. And it also over-writes my own topology file. My question is : 1. How can I preparea .gro file using my own topogy file from my PDB file i.e How I can force the gromacs to look into my present directory in stead of looking into the shared gromacs topologies ? 2. I have one more query. What is the use of 'define' string in toplgy files? Thanks. Jagannath MOndal ___ 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] query about making a pdb file
Hi all, I am a gromacs beginner. I am dealing with a 10-residue molecule each of which is un-natural amino acid called beta-peptide. I was wondering whether there is any option of making a PDB file so that I can use it to prepare the corresponding .gro file in gromacs. I somehow could generate the cartesian coordinates of the molecule. At least, can you suggest some software which are free and have mac- version so that I can generate the coresponding PDB file of the molecule from the cartesian coordinates. Thanks, Jagannath Mondal ___ 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] query about making a pdb file
Hi, Thanks, But is it possible to get the corresponding PDB format of that molcule from pymol after drawing it? Basically, I installed the pymol. But I could not find an option for writing the corresponding PDB structure of the entire molecule Jagannath On Mar 29, 2007, at 2:07 PM, Jay Mashl wrote: PyMOL (http://pymol.sf.net) is one option for building the chain based on natural amino acids and subsequently performing mutations. Jay On Wed, 28 Mar 2007, Jagannath Mondal wrote: Date: Wed, 28 Mar 2007 23:54:27 -0500 From: Jagannath Mondal [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] query about making a pdb file Hi all, I am a gromacs beginner. I am dealing with a 10-residue molecule each of which is un-natural amino acid called beta-peptide. I was wondering whether there is any option of making a PDB file so that I can use it to prepare the corresponding .gro file in gromacs. I somehow could generate the cartesian coordinates of the molecule. At least, can you suggest some software which are free and have mac-version so that I can generate the coresponding PDB file of the molecule from the cartesian coordinates. Thanks, Jagannath Mondal ___ 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 thewww 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
