[gmx-users] choosing force field
Dear all I would like to carry out unfolding simulations of my dimeric protein and would like to know which is the better force field to work with out of gromos 96 43 or 53? Also, is gromos 96 43a1 force field redundant? When I searched the previous archive, I could see similar question was raised for gromos 96 43a3 ff and could make out that 53a6 53a7..have entirely different approach in parameterization compared to 43a3 ff. Also 43a3 would give more stable structures. So is the case with my simulations but with force field 43a1 (instead of 43a3). I could see an extra non native helix when I carried out simulations with ff 43a1 which is not present with 53a7 ff. I have no experimental data/re-sources to confirm this. Also simulations on my system has not been done before. I would like to know which out of the two simulations should I consider more reliable-43a1 or 53a7? Thanks in advance. -- 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] parallelization
Dear gromacs users I would like to run my simulations on all nodes(8) with full utilisation of all cores(2 each). I have compiled gromacs version 4.6.3 using both thread mpi and open mpi. I am using following command: mpirun -np 8 mdrun_mpi -v -s -nt 2 -s *.tpr -c *.gro But I am getting following error: Setting the total number of threads is only supported with thread-MPI and Gromacs was compiled without thread-MPI . Although during compilation I have used: cmake .. -DGMX_MPI=ON -DGMX_THREAD_MPI=ON If I dont use -nt option, I could see that all the processors(8) are utilised but I am not sure whether all cores are being utilised. For version 4.6.3 without mpi, I Know by default gromacs uses all the threads but not sure if mpi version uses all threads or not. Any help is appreciated. -- 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] g_sham
Dear all gromacs users I am creating free energy landscape using g_sham but my axis are not getting labelled. I have searched the archive and found that using xmin and xmax options we can label them. I have first created my 2D projection xvg file using g_anaeig -f *.xtc -s *.tpr -first 1 -last 2 -2d *.xvg -v *.trr and then found min and max values for both the vectors, say for vector1 min:-2.25 and max:1.83 and for vector2 min:-1.60 and max: 2.22 and then I have used: g_sham -f *.xvg -ls *.xpm -notime -xmin -2.25 -1.60 0 -xmax 1.83 2.22 0 and then converted *.xpm to *.eps using xpm2ps -f *.xpm -o *.eps -rainbow blue This way I got eps file with only one axis(x axis) labelled and following line appeared: Auto tick spacing failed for Y-axis, guessing 1.19375 I would like to ask is this way of labelling the axis correct? If yes, why didn't y axis get labelled and how to solve the problem? Thanks in advance. -- 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] parallel simulation
I would like to run one simulation in parallel so that it utilises all the available nodes and cores. For that, I have compiled gromacs with mpi enabled and also installed openmpi on my machine. I am using the following command: mpirun -np 4 mdrun_mpi -v -s *.tpr When i use top command, I get: PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22449 root 20 0 107m 59m 3152 R25 2.9 0:05.42 mdrun_mpi 22450 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22451 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22452 root 20 0 107m 59m 3152 R25 2.9 0:05.40 mdrun_mpi Similarly when i use mpirun -np 2 mdrun_mpi -v -s *.tpr, I get PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22461 root 20 0 108m 59m 3248 R 50 3.0 5:58.64 mdrun_mpi 22462 root 20 0 108m 59m 3248 R 50 3.0 5:58.56 mdrun_mpi If I look at %CPU column, it is actually 100/(no. of processes) Why is all the cpu not 100% utilised? Also if I compare my performance, it is significantly hampered. Please suggest me the way so that I can run one simulation on all available nodes, cores and threads. Thanks in advance. -- 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] Re: parallel simulation
To add : I am running simulations on institute cluster with 8 nodes (2 cores each). Please suggest me the way so that I can run one simulation on all available nodes, cores and threads. Thanks in advance. On Mon, Oct 7, 2013 at 1:55 PM, pratibha kapoor kapoorpratib...@gmail.comwrote: I would like to run one simulation in parallel so that it utilises all the available nodes and cores. For that, I have compiled gromacs with mpi enabled and also installed openmpi on my machine. I am using the following command: mpirun -np 4 mdrun_mpi -v -s *.tpr When i use top command, I get: PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22449 root 20 0 107m 59m 3152 R25 2.9 0:05.42 mdrun_mpi 22450 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22451 root 20 0 107m 59m 3152 R25 2.9 0:05.41 mdrun_mpi 22452 root 20 0 107m 59m 3152 R25 2.9 0:05.40 mdrun_mpi Similarly when i use mpirun -np 2 mdrun_mpi -v -s *.tpr, I get PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 22461 root 20 0 108m 59m 3248 R 50 3.0 5:58.64 mdrun_mpi 22462 root 20 0 108m 59m 3248 R 50 3.0 5:58.56 mdrun_mpi If I look at %CPU column, it is actually 100/(no. of processes) Why is all the cpu not 100% utilised? Also if I compare my performance, it is significantly hampered. Please suggest me the way so that I can run one simulation on all available nodes, cores and threads. Thanks in advance. -- 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] principal component analysis
Dear all users I would like to calculate pc loadings for various integrated factors in the form of following sample table: Integrated Factors PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 Total non polar surface area 0.60 -0.07 -0.76 -0.11 0.08 0.05 -0.16 0.08 -0.01 0.02 Native contacts Some value Some value Some value Some value Some value Some value Some value Some value Some value Some value Content of helix Some value Some value Some value Some value Some value Some value Some value Some value Some value Some value Average volume of cavity Some value Some value Some value Some value Some value Some value Some value Some value Some value Some value Content of turns Some value Some value Some value Some value Some value Some value Some value Some value Some value Some value I have done cartesian coordinate pca using g_covar and g_anaeig (using -s and -f flags) in which I have supplied my reference structure file (which contains atomic coordinates of structure after equilibration). This way I could get eigenvalues, eigenvectors and principal components. Now I would like to ask how can I disect these principal components in terms of various properties such as those enlisted above. Any help is appreciated. -- 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] principal component analysis
Dear all gmx users I would like to calculate pc loadings for various integrated factors in the form of following sample table: Integrated factorsPC1PC2PC3 PC4PC5PC6PC7PC8 PC9PC10Total nonpolar surface area0.60 -0.07-0.76-0.11-0.060.11 0.05-0.160.06-0.02Chain exposed area 0.92 -0.14-0.050.12 0.230.200.09-0.07-0.03 0.08Chain buried area0.74-0.30-0.41 0.120.240.260.05 0.03-0.060.21Chain unpolar exposed area 0.71-0.08-0.630.02 0.03 0.280.00-0.060.08-0.03 Chain unpolar buried area0.69-0.23-0.580.06 0.12 0.17-0.100.20-0.16 -0.01Main chain B factor0.120.77-0.06 0.62-0.01-0.01-0.080.01 0.050.04Side chain B factor0.07 0.74-0.050.66-0.01 0.01-0.030.000.100.01Whole chain B factor 0.090.75-0.050.64 -0.010.00-0.050.010.08 0.02Average number of cavities-0.02 -0.43 0.72-0.090.340.10-0.19 0.170.310.09Average volume of cavity -0.040.14 0.63-0.47-0.48 0.350.020.11-0.010.06 Content of Helix 0.870.090.00-0.41 0.17 -0.10-0.09-0.12 0.130.00and so on.. Please suggest me the way to proceed. I have done cartesian principal component analysis using g_covar -f *.xtc -s *.tpr and using g_anaeig This way I could get principal components. But then how to dissect each pc in terms of above integrated factors? Any help is appreciated. -- 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
