[gmx-users] PMF plot against distance
Dear Sir I have been working in umbrella sampling to analyse protein-ligand interaction and calculate Potential Mean Force (PMF). I have generated the following his.xvg file and have provided in the attachment. I request you to kindly guide me as to how to plot against distance. I also have the query as to how far the result obtain is correct. Regards Arunima -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Standard residue of C4S shown as missing in residue topology database
On 2/19/14, 11:48 PM, Libin wrote: Hi, I downloaded chondroitin 4 sulfate from online PDB data bank and gave it as input to pdb2gmx. But, it is showing error as GC4, ASG and BDP are missing in residue topology database. I have found that these are residue names that are commonly used. So, is it wise to add the residue to the rtp file? or is there any other option. Please advise. Also, if I need to add it to rtp file, from where can I get the necessary data to be added? http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs insatallation on centos 6
On 2/20/14, 12:07 AM, Archana Sonawani-Jagtap wrote: Hi everyone, I want to install gromacs 4.5.4 on centos 6. Can anyone help me out in this. Any particular reason you want to install a very outdated version? In any case: http://www.gromacs.org/Documentation/Installation_Instructions_4.5 -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fwd: Segmentation fault with mdrun
-- Forwarded message -- From: Pavan Kumar kumar.pavan...@gmail.com Date: Thu, Feb 20, 2014 at 3:34 PM Subject: Segmentation fault with mdrun To: gromacs.org_gmx-users-requ...@maillist.sys.kth.se Hello, I am using gromacs 4.6.5. I am running my code on the cluster providing 8 nodes and 4 processor each. I am getting Segmentation Fault while running mdrunmpi My command *mpirun -n 8 mdrunmpi.4.6.5 -v -deffnm em* More Details: *Machine : GNU/Linux x86_64* *gcc (GCC) 4.3.3 * *cmake version 2.8.3* Compilation Details: *I have compiled my code using mpich compiler * *cmake .. -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_C_COMPILER=/opt/mpich2/gnu/bin/mpicc -DGMX_BUILD_OWN_FFTW=ON -DGMX_CPU_ACCELERATION=SSE2 -DCMAKE_INSTALL_PREFIX=/home/garuda/garuda3/gromacs465* If there is any problem in compiling the code itself, what is the error and how it could be corrected. Please give me any solutions, why i am getting the above error. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] conversion xtc to xyz format with openbabel
Hello all, My apologies for these out topic questions Does anybody have already try to convert xtc trajectory into xyz with openbabel? Btw, it seems that pdb file generated with editconf can not be read by openbabel. I obtain the following error : WARNING: Problems reading a PDB file Problems reading a HETATM or ATOM record. According to the PDB specification, columns 77-78 should contain the element symbol of an atom. but OpenBabel found ' ' (atom 1) Does anybody have a workaround? Thanks in advance Stéphane Abel, PhD CEA Saclay DSV/IbItec-S/SB2SM CNRS UMR 8221 Bat 528 Door 138C Gif-sur-Yvette, F-91191 FRANCE Phone (portable) : +33 6 49 37 70 60 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Is cholesterol model available in Charmm36 ff?
Dear All, A search for cholesterol model (cholesterol or CHL1 keywords) among the files of the CHARMM36 force field for Gromacs available at http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jan2014.ff.tgz; does not seem to give any result. Is the cholesterol model indeed still missing or is it present under a different name? Thanks very much in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs insatallation on centos 6
On 20.02.2014 12:40, Archana Sonawani-Jagtap wrote: I have done most of the simulations using this version. However, I had to format my PC and have centos 6. Does it matter a lot if I compare simulations run using different versions of gromacs for publication. There is always a non-zero probability that changes in the implementations in new versions may lead to significantly different results when using force fields parametrized around problems of older versions. I can remember one case discussed in this group a while ago: simulation of a DPPC lipid layer in the liquid phase in 4.0.4 resulted in a gel phase (at same temperature, same parameters) with 4.5.x/4.6.x (I'm not sure about the correct version numbers but you get the point). If you compare across different gromacs versions then you should be *absolutely sure* that your results of significance don't differ accross versions. Otherwise, you have a small, but existing chance to get wrong results and end up with wrong conclusions. Regards M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding error after equilibration of protein in membrane using g_membed
Original Message Hello everyone, I was trying to simulate a protein with POPC membrane. Initially I embedded the protein using InflateGro. But I found that the protein is coming out of the membrane after energy minimization. Then I tried embedding the protein using g_membed. I have successfully created the membedded.gro file. But I am unable to perform the equilibration of membedded.gro. The following error is coming: 3362 3363 177.6 79.3930 763.1334 0.1000 3315 3317 34.10.1473 0.1752 0.1470 3323 3325 30.40.1383 17.5395 0.1470 3323 3324 125.30.1025 3.2656 0.1000 3325 3338 151.80.0795 79.4458 0.1530 3325 3326 71.70.1390 15.3016 0.1530 3326 3327 156.20.1581 1.1020 0.1530 3327 3330 54.10.1391 0.2455 0.1390 3327 3328 52.10.1390 0.2461 0.1390 3328 3329 36.50.1095 0.1503 0.1090 3330 3331 36.70.1095 0.1503 0.1090 3317 3321 46.40.1534 0.4786 0.1530 3317 3318 33.70.1532 0.1795 0.1530 58 60 58.00.1538 0.2040 0.1530 58 59 64.00.1538 0.1839 0.1530 56 61 40.50.1830 6.3293 0.1530 57 58 133.90.1615 0.8789 0.1530 3367 3368 161.80.6755 12.2433 0.1470 3368 3370 68.00.1407 2.3025 0.1340 3368 3369 73.50.1046 2.2549 0.1000 3370 3374 109.90.1390 0.1579 0.1340 3370 3371 113.20.1390 0.1716 0.1340 3371 3373 32.70.1020 0.1239 0.1000 3371 3372 36.70.1019 0.1287 0.1000 3374 3376 36.90.1020 0.0890 0.1000 3374 3375 32.50.1020 0.1040 0.1000 3344 3346 145.21.4090 50.3186 0.1250 3344 3345 141.01.1783 49.6550 0.1250 Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms nan, max 8994748.00 (between atoms 3467 and 3473) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms nan, max 9896299.00 (between atoms 3473 and 3475) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1027 1029 80.00.1628 0.4962 0.1530 1029 1031 91.60.1905 94.7225 0.1330 1029 1030 52.40.1287 0.5485 0.1230 1034 1035 145.50.3021 118.3949 0.1430 1035 1036 173.40.1196 20.7800 0.1000 1067 1068 176.7 6396.4849 70276.0625 0.1530 1097 1101 70.90.1558 0.1831 0.1530 1097 1098 50.70.1557 0.2183 0.1530 1098 1099 39.00.1435 0.1854 0.1430 1043 1045 158.4 11.4145 1041.2142 0.1530 1043 1044 150.0 11.9767 1018.3463 0.1530 1042 1043 157.3 81.1932 3922.5566 0.1530 1041 1042 163.9 500.7729 14738.6416 0.1530 1041 1046 171.8 1984.2490 40043.3125 0.1530 1046 1048 175.5 5699.0430 88511.3906 0.1330 1048 1050 178.5 12653.2900 165113.2812 0.1470 1048 1049 174.3 5127.7061 74541.0234 0.1000 1046 1047 169.5 1938.5477 35866.9961 0.1230 1039 1041 165.4 553.3626 15883.6680 0.1470 1039 1040 164.8 156.1187 5462.1333 0.1000 1037 1039 167.3 161.4083 6334.0361 0.1330 1037 1038 175.0 32.8745 2147.0396 0.1230 1033 1037 178.0 33.8587 2314.0547 0.1530 1059 1062 179.5 18192.7480 184929.7969 0.1530 1059 1060 179.5 19682.1738 199918.0312 0.1430 1058 1059 179.8 38061.2305 389832.3438 0.1530 1058 1063 179.9 41080.1953 421760.1250 0.1530 1063 1065 179.5 28743.8848 295256.3750 0.1330 1065 1067 178.4 15112.5137 157087.1250 0.1470 1067 1068 176.7 6396.4849 70275.3828 0.1530 1065 1066 178.6 13732.9023 141496.9062 0.1000 1063 1064 179.9 21944.2773 224613.9531 0.1230 1056 1058 179.6 42098.2578 438310.9688 0.1470 1056 1057 179.4 23186.8711 244949.2344 0.1000 1054 1056 179.5 32193.0605 348201.0625 0.1330 1054 1055 179.5 16681.6074 186207.7344 0.1230 1050 1054 179.8 21997.8457 29.5781 0.1530 1050 1051 178.3 11284.8789 140964.5000 0.1530 1060 1061 179.2 6210.7412 62744.3984 0.1000 5 10 110.90.1174 17.8747 0.1530 5 6 43.40.1868 1.5629 0.1530 10 12 162.32.3017 103.0781 0.1330 10 11 56.20.1267 18.4563 0.1230 12 14 123.5 14.2793 574.0925
[gmx-users] Segmentation Fault with mdrun_mpi
Hello, I am using gromacs 4.6.5. I am running my code on the cluster providing 8 nodes and 4 processor each. I am getting Segmentation Fault while running mdrunmpi My command *mpirun -n 8 mdrunmpi.4.6.5 -v -deffnm em* More Details: *Machine : GNU/Linux x86_64* *gcc (GCC) 4.3.3* *cmake version 2.8.3* Compilation Details: *I have compiled my code using mpich compiler * *cmake .. -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_C_COMPILER=/opt/mpich2/gnu/bin/mpicc -DGMX_BUILD_OWN_FFTW=ON -DGMX_CPU_ACCELERATION=SSE2 -DCMAKE_INSTALL_PREFIX=/home/garuda/garuda3/gromacs465* mdrun log file is attached. Please find the attachment. If there is any problem in compiling the code itself, what is the error and how it could be corrected. Please give me any solutions, why i am getting the above error. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 Log file opened on Thu Feb 20 17:52:25 2014 Host: compute-1-21.local pid: 7187 nodeid: 0 nnodes: 8 Gromacs version:VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: SSE2 FFT library:fftw-3.3.2-sse2 Large file support: enabled RDTSCP usage: disabled Built on: Tue Feb 4 14:40:23 IST 2014 Built by: garuda3@compute-1-0.local [CMAKE] Build OS/arch: Linux 2.6.18-53.1.4.el5 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU X5460 @ 3.16GHz Build CPU family: 6 Model: 23 Stepping: 6 Build CPU features: apic clfsh cmov cx8 cx16 lahf_lm mmx msr pdcm pse sse2 sse3 sse4.1 ssse3 C compiler: /opt/mpich2/gnu/bin/mpicc GNU gcc (GCC) 4.1.2 20070626 (Red Hat 4.1.2-14) C compiler flags: -msse2-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG :-) G R O M A C S (-: GROtesk MACabre and Sinister :-) VERSION 4.6.5 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) ./bin/mdrun_mpi (-: PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 --- Thank You --- Input Parameters: integrator = steep nsteps = 500 init-step= 0 cutoff-scheme= Verlet ns_type = Grid nstlist = 1 ndelta = 2 nstcomm = 100 comm-mode= Linear nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy= 100 nstenergy= 1000 nstxtcout= 0 init-t = 0 delta-t = 0.001 xtcprec = 1000 fourierspacing = 0.12 nkx
Re: [gmx-users] Is cholesterol model available in Charmm36 ff?
On 2/20/14, 7:18 AM, Davit Hakobyan wrote: Dear All, A search for cholesterol model (cholesterol or CHL1 keywords) among the files of the CHARMM36 force field for Gromacs available at http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jan2014.ff.tgz; does not seem to give any result. Is the cholesterol model indeed still missing or is it present under a different name? It is not present in the Gromacs force field files. That is because of the way the CHARMM force field files are organized. I'll get it included in the next release. You can extract the parameters you need for CHL1 from toppar_all36_lipid_cholesterol.str in the CHARMM force field files; conversion to .itp should be relatively easy. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding error after equilibration of protein in membrane using g_membed
On 2/20/14, 7:44 AM, shalin...@iitg.ernet.in wrote: Original Message Hello everyone, I was trying to simulate a protein with POPC membrane. Initially I embedded the protein using InflateGro. But I found that the protein is coming out of the membrane after energy minimization. Then I tried If that's happening, it means you didn't position the protein correctly or the box is of insufficient size to accommodate the system. Large movements during EM should not happen. embedding the protein using g_membed. I have successfully created the membedded.gro file. But I am unable to perform the equilibration of membedded.gro. The following error is coming: 3362 3363 177.6 79.3930 763.1334 0.1000 3315 3317 34.10.1473 0.1752 0.1470 3323 3325 30.40.1383 17.5395 0.1470 3323 3324 125.30.1025 3.2656 0.1000 3325 3338 151.80.0795 79.4458 0.1530 3325 3326 71.70.1390 15.3016 0.1530 3326 3327 156.20.1581 1.1020 0.1530 3327 3330 54.10.1391 0.2455 0.1390 3327 3328 52.10.1390 0.2461 0.1390 3328 3329 36.50.1095 0.1503 0.1090 3330 3331 36.70.1095 0.1503 0.1090 3317 3321 46.40.1534 0.4786 0.1530 3317 3318 33.70.1532 0.1795 0.1530 58 60 58.00.1538 0.2040 0.1530 58 59 64.00.1538 0.1839 0.1530 56 61 40.50.1830 6.3293 0.1530 57 58 133.90.1615 0.8789 0.1530 3367 3368 161.80.6755 12.2433 0.1470 3368 3370 68.00.1407 2.3025 0.1340 3368 3369 73.50.1046 2.2549 0.1000 3370 3374 109.90.1390 0.1579 0.1340 3370 3371 113.20.1390 0.1716 0.1340 3371 3373 32.70.1020 0.1239 0.1000 3371 3372 36.70.1019 0.1287 0.1000 3374 3376 36.90.1020 0.0890 0.1000 3374 3375 32.50.1020 0.1040 0.1000 3344 3346 145.21.4090 50.3186 0.1250 3344 3345 141.01.1783 49.6550 0.1250 Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms nan, max 8994748.00 (between atoms 3467 and 3473) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms nan, max 9896299.00 (between atoms 3473 and 3475) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1027 1029 80.00.1628 0.4962 0.1530 1029 1031 91.60.1905 94.7225 0.1330 1029 1030 52.40.1287 0.5485 0.1230 1034 1035 145.50.3021 118.3949 0.1430 1035 1036 173.40.1196 20.7800 0.1000 1067 1068 176.7 6396.4849 70276.0625 0.1530 1097 1101 70.90.1558 0.1831 0.1530 1097 1098 50.70.1557 0.2183 0.1530 1098 1099 39.00.1435 0.1854 0.1430 1043 1045 158.4 11.4145 1041.2142 0.1530 1043 1044 150.0 11.9767 1018.3463 0.1530 1042 1043 157.3 81.1932 3922.5566 0.1530 1041 1042 163.9 500.7729 14738.6416 0.1530 1041 1046 171.8 1984.2490 40043.3125 0.1530 1046 1048 175.5 5699.0430 88511.3906 0.1330 1048 1050 178.5 12653.2900 165113.2812 0.1470 1048 1049 174.3 5127.7061 74541.0234 0.1000 1046 1047 169.5 1938.5477 35866.9961 0.1230 1039 1041 165.4 553.3626 15883.6680 0.1470 1039 1040 164.8 156.1187 5462.1333 0.1000 1037 1039 167.3 161.4083 6334.0361 0.1330 1037 1038 175.0 32.8745 2147.0396 0.1230 1033 1037 178.0 33.8587 2314.0547 0.1530 1059 1062 179.5 18192.7480 184929.7969 0.1530 1059 1060 179.5 19682.1738 199918.0312 0.1430 1058 1059 179.8 38061.2305 389832.3438 0.1530 1058 1063 179.9 41080.1953 421760.1250 0.1530 1063 1065 179.5 28743.8848 295256.3750 0.1330 1065 1067 178.4 15112.5137 157087.1250 0.1470 1067 1068 176.7 6396.4849 70275.3828 0.1530 1065 1066 178.6 13732.9023 141496.9062 0.1000 1063 1064 179.9 21944.2773 224613.9531 0.1230 1056 1058 179.6 42098.2578 438310.9688 0.1470 1056 1057 179.4 23186.8711 244949.2344 0.1000 1054 1056 179.5 32193.0605 348201.0625 0.1330 1054 1055 179.5 16681.6074 186207.7344 0.1230 1050 1054 179.8 21997.8457 29.5781 0.1530 1050 1051 178.3 11284.8789 140964.5000 0.1530 1060
[gmx-users] hybrid CPU/GPU nodes
Hallo, we are evaluating the possibility of expanding our cluster with hybrid CPU/GPU node. Which could be the better proportion CPUcores/GPU on the same nodeto obtain the best performance of Gromacs 4.6? Thank you in advance, Gloria Saracino -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding error after equilibration of protein in membrane using g_membed
On 2/20/14, 8:46 AM, shalin...@iitg.ernet.in wrote: Hello... Thanks justinI have used POPC 128 for embedding protein. While embedding the protein using g_membed, it was found that 123 lipids are overlapping the protein and 10 of them are deleted. Should I use POPC 256 for simulation. Or should i try placing the protein in differently in POPC128a itself. Kindly suggest. What should I do to place the protein symmetrically in membrane. No clue. I don't know anything about your protein. Visualization should indicate very obviously whether the membrane patch is of sufficient size. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding error after equilibration of protein in membrane using g_membed
I am attaching the membedded.gro which was created using g_membed...Kindly suggest.. Thanks On 2/20/14, 8:46 AM, shalin...@iitg.ernet.in wrote: Hello... Thanks justinI have used POPC 128 for embedding protein. While embedding the protein using g_membed, it was found that 123 lipids are overlapping the protein and 10 of them are deleted. Should I use POPC 256 for simulation. Or should i try placing the protein in differently in POPC128a itself. Kindly suggest. What should I do to place the protein symmetrically in membrane. No clue. I don't know anything about your protein. Visualization should indicate very obviously whether the membrane patch is of sufficient size. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Shalini Singh Research Scholar Department of Biotechnology IIT Guwahati Guwahati Assam-781039-- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Cationic Dummy atom method
Thank you very much Andrea. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] parameters of ligand for force field OPLS
hi GMX users can i use acpype program for ligand preparation in simulation by gromacs? how can i produce the parameters of ligand for force field OPLS? thanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding error after equilibration of protein in membrane using g_membed
On 2/20/14, 9:47 AM, shalin...@iitg.ernet.in wrote: I am attaching the membedded.gro which was created using g_membed...Kindly suggest.. The box is much too small in the z-direction. Your protein is overlapping with itself, leading to the crash. You may need a larger membrane patch, but you definitely need to increase the box size along z. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] parameters of ligand for force field OPLS
Also, have look to here: http://gromacs.5086.x6.nabble.com/after-using-ACPYPE-GROMACS-OPLS-itp-file-generated-an-atom-type-like-opls-x-with-mass-0-000-td5012336.html cheers and On 20/02/2014 22:30, Mahboobeh Eslami wrote: hi GMX users can i use acpype program for ligand preparation in simulation by gromacs? how can i produce the parameters of ligand for force field OPLS? thanks a lot -- Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fwd: Segmentation fault with mdrun
My only guess is that your compiler and/or MPICH version are broken. We certainly don't test on it. There's many reasons the install guide for 4.6 says to get the latest version of your compiler of choice. Mark On Thu, Feb 20, 2014 at 12:35 PM, Pavan Kumar kumar.pavan...@gmail.comwrote: -- Forwarded message -- From: Pavan Kumar kumar.pavan...@gmail.com Date: Thu, Feb 20, 2014 at 3:34 PM Subject: Segmentation fault with mdrun To: gromacs.org_gmx-users-requ...@maillist.sys.kth.se Hello, I am using gromacs 4.6.5. I am running my code on the cluster providing 8 nodes and 4 processor each. I am getting Segmentation Fault while running mdrunmpi My command *mpirun -n 8 mdrunmpi.4.6.5 -v -deffnm em* More Details: *Machine : GNU/Linux x86_64* *gcc (GCC) 4.3.3 * *cmake version 2.8.3* Compilation Details: *I have compiled my code using mpich compiler * *cmake .. -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_C_COMPILER=/opt/mpich2/gnu/bin/mpicc -DGMX_BUILD_OWN_FFTW=ON -DGMX_CPU_ACCELERATION=SSE2 -DCMAKE_INSTALL_PREFIX=/home/garuda/garuda3/gromacs465* If there is any problem in compiling the code itself, what is the error and how it could be corrected. Please give me any solutions, why i am getting the above error. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Is it possible to output the force/energy associated with each position restraint?
Only by constructing matching .tpr and trajectory subsets (tpbconv -n and trjconv -n) and then using mdrun -rerun to get the position restraint re-calculation to refer to only one. Mark On Thu, Feb 20, 2014 at 4:28 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/19/14, 7:39 PM, Ling Liu wrote: Say I have five atoms that have position restraints in a system. I understand that I can output the total energy associated with all position restraints using g_energy. But is there a way to output energy (0.5*k*dx^2) or force (k*dx) that is associated with each of these five position restraints. Not individually, but it's a trivial calculation to do based on displacements over time. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Public server of gromacs to share my files
Dear sir I have generated the plot for Umbrella potential. I have calculated the potential mean force (PMF) between Protein-Ligand. I would like to share my graph over public server. I request you to provide the link where I can share my result. Regards Arunima -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
