[gmx-users] coupling to center of mass
How to apply temp coupling only to the center-of-mass motion of water molecules in mdp file. -- Sree lakshmi ramesh Ph.D student Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology, Hyderabad Gachibowli, Hyderabad 500032 ph: +91 40 66531919 mob:+91 9502753353 -- 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] OpenSuse 12.1 + CUDA Installation Error
On 25.07.2013 04:25, Carlos Bueno wrote: I added all the repositories and installed all you told me. And that solved the problem for one of the computers The others still have an error in make: [ 55%] Building NVCC (Device) object src/mdlib/nbnxn_cuda/./nbnxn_cuda_generated_nbnxn_cuda.cu.o /home/cuda2/Programas/gromacs-4.6.3/include/types/nbnxn_pairlist.h(216): error: identifier nbnxn_alloc_t is undefined /home/cuda2/Programas/gromacs-4.6.3/include/types/nbnxn_pairlist.h(217): error: identifier nbnxn_free_t is undefined 2 errors detected in the compilation of /tmp/tmpxft_76ad_-11_nbnxn_cuda.compute_20.cpp2.i. CMake Error at CMakeFiles/nbnxn_cuda_generated_nbnxn_cuda.cu.o.cmake:256 (message): Can you look in the first part of your cmake log to find out which gcc version has been used? What does `g++ -v` say? M. -- 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] Rotation Constraints - PMF - external potential
On Jul 24, 2013, at 5:53 PM, battis...@libero.it wrote: Dear Carsten could you give me more information about your suggestions? I tried but probably I did not understand well what you meant. Hi Anna, I suggested to use the enforced rotation module of Gromacs 4.6 to restrain the orientation of your molecule(s). If you want to use the orientation restraints module instead, I am afraid I can not help you much with that, maybe someone else on this list? In order to avoid the rotation of the structure A and of the structure B, I have defined into the index file a group A_B that contains A+B and I have setted in the mdp file the following parameters: ; Orientation restraints: No or Yes orire= yes ; Orientation restraints force constant and tau for time averaging orire-fc = 500 orire-tau= 100 orire-fitgrp = A_B ; Output frequency for trace(SD) and S to energy file nstorireout = 100 As I have synthetically described in the first post , the structures A and B (characterized by a cylindrical shape) are defined by a number of 32 unit- structures that I call s. Into the itp is defined the topology for the s structure, and so in order to put an orientation restraints between atoms that are not included into the same itp file, I cannot put into the topology a section like that described into the manual 4.6.2 pag. 92 namely, [ orientation_restraints ], could I ? Could you tell me How I can fix the orientation of the systems A and B? Using the enforced rotation module you would choose an index group and an axis for each group that you want to fix the orientation, set the rotation angle to zero and choose an appropriate force constant. Appropriate potential functions would be the pivot-free ones if I understand your setting correctly. I don't understand the manual's explanation about the orire-fitgrp: (fit group for orientation restraining. This group of atoms is used to determine the rotation R of the system with respect to the reference orientation. The reference orientation is the starting conformation of the first subsystem. For a protein, backbone is a reasonable choice) How one have to give the group? using an index file or defining the group in the topology? This is the orire-fitgrp = A_B mdp file setting that you made. Best, Carsten Messaggio originale Da: ckut...@gwdg.de Data: 23/07/2013 13.09 A: battis...@libero.itbattis...@libero.it, Discussion list for GROMACS usersgmx-users@gromacs.org Ogg: Re: [gmx-users] Rotation Constraints - PMF Hi Anna, please have a look at the Enforced Rotation Section in the Gromacs 4.6 manual. You can restrain the angle of rotation about an axis by setting the rotation rate to zero. There is also a 4.5 add-on available with rotational restraints in the Gromacs git repository (branch rotation). For more info you may want to look at this page: http://www.mpibpc.mpg.de/grubmueller/rotation Best, Carsten On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote: Dear user and expert, I'd like ask you a suggestion about a problem that I will try present you schematically. I have got a structure s and I have generated the topolgy file itp for it. A number of separate s in turn generate a complex structure A, that is characterized by a cylindrical shape. Now, I constructed a system with two cylindrical structures, A and B (in total made by 64 s structures), and I'd like make an Umbrella Sampling calculation in order to study the PMF varying the distance between A and B. My problem is that I'd like fix the orientation of the axis of each structure A and B long the z axis, during the dynamics. So I need to put a force into the system or a constrain, such that when the axis of A or B rotates respect to z axis, the force puts back the axis of the structure in the z direction. It this possible? If it is so, could you tell me how to do that? Than you very much, Anna -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax:
RE: [gmx-users] Calculate interaction energy dynamically
Date: Wed, 24 Jul 2013 09:35:26 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Calculate interaction energy dynamically On 7/24/13 9:25 AM, Davit Hakobyan wrote: Thank you again for your time and help. Performing rerun on the original system passes without warnings with the following output: Option Filename Type Description -s inp/dyn/dppc_dupc_chol_034x051x015_295K.tpr InputRun input file: tpr tpb tpa -o /scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K_testrerun.trr Output Full precision trajectory: trr trj cpt -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi state.cpt Input, Opt. Checkpoint file -cpo state.cpt Output, Opt. Checkpoint file -c crd/dynmc_end/dppc_dupc_chol_034x051x015_295K_testrerun.gro Output Structure file: gro g96 pdb etc. -e dat/enr/dppc_dupc_chol_034x051x015_295K_testrerun.edr Output Energy file -g out/dppc_dupc_chol_034x051x015_295K_testrerun.log Output Log file -dhdl dhdl.xvg Output, Opt. xvgr/xmgr file -fieldfield.xvg Output, Opt. xvgr/xmgr file -tabletable.xvg Input, Opt. xvgr/xmgr file -tablep tablep.xvg Input, Opt. xvgr/xmgr file -tableb table.xvg Input, Opt. xvgr/xmgr file -rerun /scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K.trr Input, Opt! Trajectory: xtc trr trj gro g96 pdb cpt -tpitpi.xvg Output, Opt. xvgr/xmgr file -tpid tpidist.xvg Output, Opt. xvgr/xmgr file -eisam.edi Input, Opt. ED sampling input -eosam.edo Output, Opt. ED sampling output -j wham.gct Input, Opt. General coupling stuff -jobam.gct Output, Opt. General coupling stuff -ffout gct.xvg Output, Opt. xvgr/xmgr file -devout deviatie.xvg Output, Opt. xvgr/xmgr file -runav runaver.xvg Output, Opt. xvgr/xmgr file -px pullx.xvg Output, Opt. xvgr/xmgr file -pf pullf.xvg Output, Opt. xvgr/xmgr file -mtx nm.mtx Output, Opt. Hessian matrix -dn dipole.ndx Output, Opt. Index file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -deffnm string Set the default filename for all file options -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -nt int0 Number of threads to start (0 is guess) -npmeint-1 Number of separate nodes to be used for PME, -1 is guess -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -[no]ddcheck bool yes Check for all bonded interactions with DD -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum autoDynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -gcomint-1 Global communication frequency -[no]v bool no Be loud and noisy -[no]compact bool yes Write a compact log file -[no]seppot bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -pforce real -1 Print all forces larger than this (kJ/mol nm) -[no]reprod bool no Try to avoid optimizations that affect binary reproducibility -cpt real 15 Checkpoint interval (minutes) -[no]cpnum bool no Keep and number checkpoint files -[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names -maxhreal -1 Terminate after 0.99 times this time (hours) -multi int0 Do multiple simulations in parallel -replex int0 Attempt replica exchange every # steps -reseed int-1 Seed for replica exchange, -1 is generate a seed -[no]ionize bool
[gmx-users] Any chance to get mkl linked in 4.6.3 by any wizardry? (Linux/Intel64)
I read the report (http://redmine.gromacs.org/issues/1110)
and tried some combinations. This was my last failing
attempt:
- - - 8 - - - - - - - - - - - - - - - - - - - - - - - - - -
#!/bin/sh
export GMXVERSION=gromacs-4.6.3
export GMXTARGET=/opt/gromacs463
MINC=/opt/intel/mkl/include
MLIB=/opt/intel/mkl/lib/intel64
ILIB=/opt/intel/composerxe/lib/intel64
#
cmake ../${GMXVERSION} \
-DGMX_FFT_LIBRARY=mkl-DMKL_LIBRARIES=${MLIB}/libmkl_intel_ilp64.so;${MLIB}/libmkl_core.so;${MLIB}/libmkl_intel_thread.so;${ILIB}/libiomp5.so
\
-DCMAKE_CXX_COMPILER=icpc\
-DCMAKE_C_COMPILER=icc \
-DMKL_INCLUDE_DIR=${MINC}\
-DCMAKE_INSTALL_PREFIX=${GMXTARGET} \
-DGMX_X11=OFF
- - - - 8 - - - - - - - - - - - - - - - - - - - - - - - - - -
ICC version is 13.1.1 (with mkl included).
4.6.2 worked. Does anybody have a spell for 4.6.3?
Thanks regards
M.
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Re: [gmx-users] Any chance to get mkl linked in 4.6.3 by any wizardry? (Linux/Intel64)
What doesn't work about the install guide instructions: 'Using MKL
with icc 11 or higher is very simple. Set up your compiler environment
correctly, perhaps with a command like source /path/to/compilervars.sh
intel64 (or consult your local documentation). Then set
-DGMX_FFT_LIBRARY=mkl when you run CMake.'
Mark
On Thu, Jul 25, 2013 at 12:08 PM, Mirco Wahab
mirco.wa...@chemie.tu-freiberg.de wrote:
I read the report (http://redmine.gromacs.org/issues/1110)
and tried some combinations. This was my last failing
attempt:
- - - 8 - - - - - - - - - - - - - - - - - - - - - - - - - -
#!/bin/sh
export GMXVERSION=gromacs-4.6.3
export GMXTARGET=/opt/gromacs463
MINC=/opt/intel/mkl/include
MLIB=/opt/intel/mkl/lib/intel64
ILIB=/opt/intel/composerxe/lib/intel64
#
cmake ../${GMXVERSION} \
-DGMX_FFT_LIBRARY=mkl-DMKL_LIBRARIES=${MLIB}/libmkl_intel_ilp64.so;${MLIB}/libmkl_core.so;${MLIB}/libmkl_intel_thread.so;${ILIB}/libiomp5.so
\
-DCMAKE_CXX_COMPILER=icpc\
-DCMAKE_C_COMPILER=icc \
-DMKL_INCLUDE_DIR=${MINC}\
-DCMAKE_INSTALL_PREFIX=${GMXTARGET} \
-DGMX_X11=OFF
- - - - 8 - - - - - - - - - - - - - - - - - - - - - - - - - -
ICC version is 13.1.1 (with mkl included).
4.6.2 worked. Does anybody have a spell for 4.6.3?
Thanks regards
M.
--
gmx-users mailing listgmx-users@gromacs.org
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--
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Re: [gmx-users] Re: Limitations of simulations?
On 7/25/13 12:44 AM, Jonathan Saboury wrote: Hm, I am probably completely wrong about this, but can you do implicit solvent and Periodic Box Conditions? That's not typical. I suppose one could do an NVT simulation, but the only stable way I have found to run in implicit solvent is to use infinite cutoffs, which precludes the use of PBC. Even long cutoffs typically do not produce reasonable energy conservation, at least in my hands. Then there's the matter of unscreened long-range interactions. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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] binding energy for membrane system
On 7/25/13 12:51 AM, Albert wrote: Hello: I notice that the manual or tutorial in Gromacs (FEP, unbralla sampling, TI and so on) website for binding energy evaluation are all for protein in water. I am just wondering how can we evaluate the protein/ligand binding affinity for membrane system accurately? Probably the most difficult thing is to evaluate the term from protein/lipids and protein/water part, since the system is heterogeneous instead of homogeneous. Have a look through the literature to see what other people do. The Gromacs manual and tutorials are not going to be definitive sources for everything, nor do they claim to be. Probably PMF is the way to go. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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] Umbrella Sampling _ pulled ion
After running for 100 ps, I visualized the pullf_umbrella.xvg, in this plot I found the F value around 100 kJ/mol/ns. But force constant which I had set in md_US.mdp file was 4000 KJ/mol/ns. Does this difference show me that the US has not done properly? ;define = -DPOSRES integrator = md ; leap-frog integrator nsteps =10 ; 1 * 10 = 100 ps dt = 0.001 ; 1 fs nstcomm = 10 tinit = 0 ; Output control nstxout = 5000 ; save coordinates every 100 ps nstvout = 5000 ; save velocities every 100 ps nstenergy = 1000 ; save energies every 2 ps nstfout = 5000 nstxtcout = 5000 ; every 10 ps continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 1.0 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ewald_rtol = 1e-5 optimize_fft = yes ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein_POPC Water_Ces_CL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = position pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = POPC pull_group1 = Ces_ion pull_init1 = 0.0 0.0 0.0 pull_rate1 = 0.0 0.0 0.00 pull_vec1 = 0 0 1 pull_k1 = 4000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution refcoord_scaling = com Would you please let me know your suggestions ? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Wednesday, July 24, 2013 9:41 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/24/13 11:53 AM, Shima Arasteh wrote: Yes, Thanks. Would you give me a hint on this fact that how I would be sure that I am running a correct US ? with proper settings? Either the restraint distance is maintained with acceptable sampling around that distance (given the force constant) or it's not. To save time, I' d prefer to run the US.mdp just for one window. Do you agree with me that if I run an incorrect US for any of the windows, I would get an odd result for npt_US or md_US? It should be pretty easy to see. -Justin Many many thanks for your time and suggestions. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, July 24, 2013 8:05 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/24/13 11:30 AM, Shima Arasteh wrote: Hi, I am trying to run US on a system composed of lipid bilayer/ ion/ water/ peptide. The peptide is inserted through the lipid bilayer and I' d like to study the ion conduction through the peptide across the membrane. In order to do so, I tried to set a specific ion ( Ces with the atom number 85563) as the pull_group1 in mdp file: pull_group1 = Ces_ion So I had to get a new group named Ces_ion contains of Ces 85563. Therefore made a new index file ( index_US.ndx). In this ndx file, there is an extra group in addition of existed groups as this( The last 2 lines in ndx file) : [ system] ... [protein] ... [protein-H] ... [ Ces_ion ] 85563 But after running the grompp, I get this fatal error: File input/output error: index_US.ndx Would you please let
Re: [gmx-users] Umbrella Sampling _ pulled ion
On 7/25/13 7:52 AM, Shima Arasteh wrote: After running for 100 ps, I visualized the pullf_umbrella.xvg, in this plot I found the F value around 100 kJ/mol/ns. But force constant which I had set in md_US.mdp file was 4000 KJ/mol/ns. Does this difference show me that the US has not done properly? Force and force constant are different. The values in the pullf.xvg file indicate the magnitude of force required to maintain the position of the restrained ion. The pullx.xvg will probably be more useful in directly determining how effective the restraining potential was. -Justin ;define= -DPOSRES integrator = md; leap-frog integrator nsteps =10 ; 1 * 10 = 100 ps dt = 0.001 ; 1 fs nstcomm = 10 tinit = 0 ; Output control nstxout = 5000 ; save coordinates every 100 ps nstvout = 5000 ; save velocities every 100 ps nstenergy = 1000 ; save energies every 2 ps nstfout = 5000 nstxtcout = 5000; every 10 ps continuation= yes; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 1.0 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ewald_rtol = 1e-5 optimize_fft= yes ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein_POPC Water_Ces_CL; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 310 310; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = position pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = POPC pull_group1 = Ces_ion pull_init1 = 0.0 0.0 0.0 pull_rate1 = 0.0 0.0 0.00 pull_vec1= 0 0 1 pull_k1 = 4000 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution refcoord_scaling= com Would you please let me know your suggestions ? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Wednesday, July 24, 2013 9:41 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/24/13 11:53 AM, Shima Arasteh wrote: Yes, Thanks. Would you give me a hint on this fact that how I would be sure that I am running a correct US ? with proper settings? Either the restraint distance is maintained with acceptable sampling around that distance (given the force constant) or it's not. To save time, I' d prefer to run the US.mdp just for one window. Do you agree with me that if I run an incorrect US for any of the windows, I would get an odd result for npt_US or md_US? It should be pretty easy to see. -Justin Many many thanks for your time and suggestions. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, July 24, 2013 8:05 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/24/13 11:30 AM, Shima Arasteh wrote: Hi, I am trying to run US on a system composed of lipid bilayer/ ion/ water/ peptide. The peptide is inserted through the lipid bilayer and I' d like to study the ion conduction through the peptide across the membrane. In order to do so, I tried to set a specific ion ( Ces with the atom number 85563) as the pull_group1 in mdp file: pull_group1 = Ces_ion So I had to get a new group named Ces_ion contains of Ces 85563. Therefore made a new index file ( index_US.ndx).
Re: [gmx-users] GROMACS 4.6.3 Static Linking
Vitaly has it upside down - it is normally required to build a static binary on Crays. cmake .. -DBUILD_SHARED_LIBS=off just works for building static binaries for me with 4.6.3 on lindgren, a Cray XE6, when using PrgEnv-gnu/4.0.46 Mark On Wed, Jul 24, 2013 at 8:58 AM, Andrew R Turner a.tur...@epcc.ed.ac.uk wrote: Hi Vitaly, Impossible just for v4.6.3? It was certainly possible to create static executables for a Cray XE using v4.6.1 (I know, because I have done it). I followed the same procedure for 4.6.3 and have only managed to get dynamic executables (which do not work) hence my question. I will have more of a dig into the build procedure but just wondered if anyone was aware of anything that has changed between these two minor versions (probably in the build process) that could have precipitated this change in behaviour. Cheers Andy Quoting Dr. Vitaly Chaban vvcha...@gmail.com on Sat, 20 Jul 2013 09:42:41 +0200: Soneone said here that static versions are impossible for Cray... Dr. Vitaly V. Chaban On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner a.tur...@epcc.ed.ac.ukwrote: Hi I am having problems creating static versions of the GROMACS binaries for a Cray XE6 (www.hector.ac.uk). The build process I am using is documented at: http://www.hector.ac.uk/**support/documentation/** software/gromacs/compiling_4-**6-1_phase3.phphttp://www.hector.ac.uk/support/documentation/software/gromacs/compiling_4-6-1_phase3.php and successfully produced static binaries for 4.6.1. Has something changed in the new version? In particular, I am setting: -DCMAKE_SKIP_RPATH=YES -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_C_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops -DCMAKE_CXX_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops but still get dynamic executables: gmx@hector-xe6-5:~/4.6.3-**phase3/bin ldd grompp linux-vdso.so.1 = (0x7fff00da2000) libm.so.6 = /lib64/libm.so.6 (0x7f50dc58f000) libpthread.so.0 = /lib64/libpthread.so.0 (0x7f50dc371000) libAtpSigHandler.so.0 = /opt/cray/lib64/**libAtpSigHandler.so.0 (0x7f50dc16b000) libgfortran.so.3 = /opt/gcc/4.7.2/snos/lib64/**libgfortran.so.3 (0x7f50dbe54000) libscicpp_gnu.so.2 = /opt/cray/lib64/libscicpp_gnu.**so.2 (0x7f50dbc4a000) libsci_gnu_mp.so.2 = /opt/cray/lib64/libsci_gnu_mp.**so.2 (0x7f50d72ec000) libstdc++.so.6 = /opt/gcc/4.7.2/snos/lib64/**libstdc++.so.6 (0x7f50d6fdf000) libfftw3_mpi.so.3 = /opt/cray/lib64/libfftw3_mpi.**so.3 (0x7f50d6dc6000) libfftw3f_mpi.so.3 = /opt/cray/lib64/libfftw3f_mpi.**so.3 (0x7f50d6bae000) libfftw3_threads.so.3 = /opt/cray/lib64/libfftw3_**threads.so.3 (0x7f50d69a6000) libfftw3f_threads.so.3 = /opt/cray/lib64/libfftw3f_**threads.so.3 (0x7f50d679d000) libfftw3.so.3 = /opt/cray/lib64/libfftw3.so.3 (0x7f50d63a2000) libfftw3f.so.3 = /opt/cray/lib64/libfftw3f.so.3 (0x7f50d5f7c000) libmpich_gnu_47.so.1 = /opt/cray/lib64/libmpich_gnu_**47.so.1 (0x7f50d5add000) libmpichf90_gnu_47.so.1 = /opt/cray/lib64/libmpichf90_**gnu_47.so.1 (0x7f50d58da000) libmpl.so.0 = /opt/cray/lib64/libmpl.so.0 (0x7f50d56d5000) librt.so.1 = /lib64/librt.so.1 (0x7f50d54cb000) libxpmem.so.0 = /opt/cray/xpmem/default/lib64/**libxpmem.so.0 (0x7f50d52c9000) libdmapp.so.1 = /opt/cray/dmapp/default/lib64/**libdmapp.so.1 (0x7f50d5092000) libugni.so.0 = /opt/cray/ugni/default/lib64/**libugni.so.0 (0x7f50d4e72000) libpmi.so.0 = /opt/cray/pmi/default/lib64/**libpmi.so.0 (0x7f50d4c51000) libalpslli.so.0 = /usr/lib/alps/libalpslli.so.0 (0x7f50d4a4e000) libalpsutil.so.0 = /usr/lib/alps/libalpsutil.so.0 (0x7f50d4849000) libudreg.so.0 = /opt/cray/udreg/default/lib64/**libudreg.so.0 (0x7f50d4641000) libgomp.so.1 = /opt/gcc/4.7.2/snos/lib64/**libgomp.so.1 (0x7f50d4432000) libc.so.6 = /lib64/libc.so.6 (0x7f50d40d3000) libgcc_s.so.1 = /opt/gcc/4.7.2/snos/lib64/**libgcc_s.so.1 (0x7f50d3ebd000) /lib/ld64.so.1 = /lib64/ld-linux-x86-64.so.2 (0x7f50dc812000) libquadmath.so.0 = /opt/gcc/4.7.2/snos/lib64/**libquadmath.so.0 (0x7f50d3c87000) libcray_memcpy.so.0 = /opt/cray/lib64/libcray_**memcpy.so.0 (0x7f50d3a84000) libopa.so.1 = /opt/cray/lib64/libopa.so.1 (0x7f50d3882000) librca.so.0 = /opt/cray/rca/default/lib64/**librca.so.0 (0x7f50d367d000) libdl.so.2 = /lib64/libdl.so.2 (0x7f50d3479000) Any ideas? Andy ==**=== Dr Andrew R. Turner e: a.tur...@epcc.ed.ac.uk skype: aturner-epcc t: +44 (0)131 651 3578 p: EPCC, University of Edinburgh EH9 3JZ
[gmx-users] Re: Umbrella Sampling _ pulled ion
Think your .mdp-file looks reasonable. If you are totaly unsure you could determine the PMF of two water molecules. As a reference one can use the radial distribution function g(r) and calculate the PMF as V_pmf(r) = -kT LN(g(r)) One side note: Since the force constant you are using is relative large you will need a relative small distance increment between the individual umbrella windows. Greatings Thomas Am 25.07.2013 13:56, schrieb gmx-users-requ...@gromacs.org: After running for 100 ps, I visualized the pullf_umbrella.xvg, in this plot I found the F value around 100 kJ/mol/ns. But force constant which I had set in md_US.mdp file was 4000 KJ/mol/ns. Does this difference show me that the US has not done properly? ;define??? ??? = -DPOSRES ??? integrator? = md??? ; leap-frog integrator nsteps? =10 ; 1 * 10 = 100 ps dt? = 0.001 ; 1 fs nstcomm = 10 tinit?? = 0 ; Output control nstxout = 5000?? ; save coordinates every 100 ps nstvout = 5000?? ; save velocities every 100 ps nstenergy?? = 1000?? ; save energies every 2 ps nstfout = 5000 nstxtcout?? = 5000??? ??? ??? ??? ; every 10 ps continuation??? = yes??? ; first dynamics run constraint_algorithm = lincs??? ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter? = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid? ; search neighboring grid cells nstlist = 5 ; 10 fs rlist?? = 1.2?? ; short-range neighborlist cutoff (in nm) rlistlong?? = 1.4 rcoulomb??? = 1.2?? ; short-range electrostatic cutoff (in nm) rvdw??? = 1.2?? ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 1.0 ; Electrostatics coulombtype = PME?? ; Particle Mesh Ewald for long-range electrostatics pme_order?? = 4 ; cubic interpolation fourierspacing? = 0.12? ; grid spacing for FFT fourier_nx? = 0 fourier_ny? = 0 fourier_nz? = 0 ewald_rtol? = 1e-5 optimize_fft??? = yes ; Temperature coupling is on tcoupl? = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein_POPC Water_Ces_CL??? ??? ; two coupling groups - more accurate tau_t?? = 0.5?? 0.5?? ??? ; time constant, in ps ref_t?? = 310?? 310??? ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl? = Parrinello-Rahman??? ; no pressure coupling in NVT pcoupltype? = semiisotropic tau_p?? = 4 ref_p?? = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz?? ; 3-D PBC ; Long-range dispersion correction DispCorr??? = EnerPres ; Pull code pull??? = umbrella pull_geometry?? = position pull_dim??? = N N Y pull_start? = yes pull_ngroups??? = 1 pull_group0 = POPC pull_group1 = Ces_ion pull_init1? = 0.0 0.0 0.0 pull_rate1? = 0.0 0.0 0.00 pull_vec1??? = 0 0 1 pull_k1 = 4000? ; kJ mol^-1 nm^-2 pull_nstxout??? = 1000? ; every 2 ps pull_nstfout??? = 1000? ; every 2 ps ; Velocity generation gen_vel = no?? ; assign velocities from Maxwell distribution refcoord_scaling??? = com Would you please let me know your suggestions ? -- 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] filling missing param values
Dear All, I am working on some molecule and I have defined atom types with OPLSaa and all atom types really exist in oplsaa and well chosen so no approximation in choosing atom types. During grompp, I found there are dihedral param missing. e.g. N CT CT NT N CT CT N3 Is there any 'good' way of finding/assuming dihedral params for this? or I should choose values of some nearby atom types? Please suggest regards, Jiomm -- 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] filling missing param values
On 7/25/13 8:25 AM, gromacs query wrote: Dear All, I am working on some molecule and I have defined atom types with OPLSaa and all atom types really exist in oplsaa and well chosen so no approximation in choosing atom types. During grompp, I found there are dihedral param missing. e.g. N CT CT NT N CT CT N3 Is there any 'good' way of finding/assuming dihedral params for this? or I should choose values of some nearby atom types? The OPLS dihedral fitting strategy is exceptionally well explained in the Kaminski 2001 paper (reference in Gromacs manual). -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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] filling missing param values
Dear Justin, Thanks this paper is quite explained and requires much detailed study (sorry am escaping!) As I have these two params missing, is there any tool that can help me in this regard or may be some approximation method I may use? thanks On Thu, Jul 25, 2013 at 3:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/25/13 8:25 AM, gromacs query wrote: Dear All, I am working on some molecule and I have defined atom types with OPLSaa and all atom types really exist in oplsaa and well chosen so no approximation in choosing atom types. During grompp, I found there are dihedral param missing. e.g. N CT CT NT N CT CT N3 Is there any 'good' way of finding/assuming dihedral params for this? or I should choose values of some nearby atom types? The OPLS dihedral fitting strategy is exceptionally well explained in the Kaminski 2001 paper (reference in Gromacs manual). -Justin -- ==** Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] filling missing param values
On 7/25/13 8:41 AM, gromacs query wrote: Dear Justin, Thanks this paper is quite explained and requires much detailed study (sorry am escaping!) As I have these two params missing, is there any tool that can help me in this regard or may be some approximation method I may use? It is very hard to assign dihedrals based on approximations, and they are generally not very transferable. Bonds and angles are easier, but dihedrals are quite complex and the types and charges on atoms i and l have a significant impact on the parameters. Shortcuts here will probably lead to a bad topology. Parameterization is a hard road that takes a lot of time, even for bonded terms that you think may be simple. -Justin thanks On Thu, Jul 25, 2013 at 3:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/25/13 8:25 AM, gromacs query wrote: Dear All, I am working on some molecule and I have defined atom types with OPLSaa and all atom types really exist in oplsaa and well chosen so no approximation in choosing atom types. During grompp, I found there are dihedral param missing. e.g. N CT CT NT N CT CT N3 Is there any 'good' way of finding/assuming dihedral params for this? or I should choose values of some nearby atom types? The OPLS dihedral fitting strategy is exceptionally well explained in the Kaminski 2001 paper (reference in Gromacs manual). -Justin -- ==** Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. 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 == -- 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] filling missing param values
Dear Justin, Parameterization is a hard road that takes a lot of time I agree and thanks for reply On Thu, Jul 25, 2013 at 3:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/25/13 8:41 AM, gromacs query wrote: Dear Justin, Thanks this paper is quite explained and requires much detailed study (sorry am escaping!) As I have these two params missing, is there any tool that can help me in this regard or may be some approximation method I may use? It is very hard to assign dihedrals based on approximations, and they are generally not very transferable. Bonds and angles are easier, but dihedrals are quite complex and the types and charges on atoms i and l have a significant impact on the parameters. Shortcuts here will probably lead to a bad topology. Parameterization is a hard road that takes a lot of time, even for bonded terms that you think may be simple. -Justin thanks On Thu, Jul 25, 2013 at 3:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/25/13 8:25 AM, gromacs query wrote: Dear All, I am working on some molecule and I have defined atom types with OPLSaa and all atom types really exist in oplsaa and well chosen so no approximation in choosing atom types. During grompp, I found there are dihedral param missing. e.g. N CT CT NT N CT CT N3 Is there any 'good' way of finding/assuming dihedral params for this? or I should choose values of some nearby atom types? The OPLS dihedral fitting strategy is exceptionally well explained in the Kaminski 2001 paper (reference in Gromacs manual). -Justin -- == Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Any chance to get mkl linked in 4.6.3 by any wizardry? (Linux/Intel64)
On 25.07.2013 12:28, Mark Abraham wrote: What doesn't work about the install guide instructions: 'Using MKL with icc 11 or higher is very simple. Set up your compiler environment correctly, perhaps with a command like source /path/to/compilervars.sh intel64 (or consult your local documentation). Then set -DGMX_FFT_LIBRARY=mkl when you run CMake.' Wow! I just checked this - and, what a nice surprise, it works. Since when don't you have to specify any mkl library in order to get the correct linking? Thank you M. -- 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] creating a checkpoint file
Dear users, For some unknown reasons checkpoint file are not being created if -cpo is not mentioned (in 4.5.3). Now I have a trajectory of ~10ns without a checkpoint file. I tried the following - tpbconv option to create a new .tpr file so that I can start form the point I stopped. But manual mentions the cpt file has to be used. So my question is - 1. Is it ok if I us the new tpr file created using tpbconv to continue the simulation 2. If not how can I create a checkpoint file now? Thank you Regards Kavya -- 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] Any chance to get mkl linked in 4.6.3 by any wizardry? (Linux/Intel64)
On Thu, Jul 25, 2013 at 2:55 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 25.07.2013 12:28, Mark Abraham wrote: What doesn't work about the install guide instructions: 'Using MKL with icc 11 or higher is very simple. Set up your compiler environment correctly, perhaps with a command like source /path/to/compilervars.sh intel64 (or consult your local documentation). Then set -DGMX_FFT_LIBRARY=mkl when you run CMake.' Wow! I just checked this - and, what a nice surprise, it works. Great, glad the new feature is useful :-) Since when don't you have to specify any mkl library in order to get the correct linking? See http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x (4.6.2) Mark -- 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] GROMACS 4.6.3 Static Linking
Mark, A bit of testing has revealed that it is the -DGMX_PREFER_STATIC_LIBS=ON flag that makes the difference. With this flag you end up with dynamic executables that do not work (I think due to some glibc problem I have not yet tracked down) whereas if I exclude this option then I get working static executables. Thanks for all your help Andy Quoting Mark Abraham mark.j.abra...@gmail.com on Thu, 25 Jul 2013 14:18:35 +0200: Vitaly has it upside down - it is normally required to build a static binary on Crays. cmake .. -DBUILD_SHARED_LIBS=off just works for building static binaries for me with 4.6.3 on lindgren, a Cray XE6, when using PrgEnv-gnu/4.0.46 Mark On Wed, Jul 24, 2013 at 8:58 AM, Andrew R Turner a.tur...@epcc.ed.ac.uk wrote: Hi Vitaly, Impossible just for v4.6.3? It was certainly possible to create static executables for a Cray XE using v4.6.1 (I know, because I have done it). I followed the same procedure for 4.6.3 and have only managed to get dynamic executables (which do not work) hence my question. I will have more of a dig into the build procedure but just wondered if anyone was aware of anything that has changed between these two minor versions (probably in the build process) that could have precipitated this change in behaviour. Cheers Andy Quoting Dr. Vitaly Chaban vvcha...@gmail.com on Sat, 20 Jul 2013 09:42:41 +0200: Soneone said here that static versions are impossible for Cray... Dr. Vitaly V. Chaban On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner a.tur...@epcc.ed.ac.ukwrote: Hi I am having problems creating static versions of the GROMACS binaries for a Cray XE6 (www.hector.ac.uk). The build process I am using is documented at: http://www.hector.ac.uk/**support/documentation/** software/gromacs/compiling_4-**6-1_phase3.phphttp://www.hector.ac.uk/support/documentation/software/gromacs/compiling_4-6-1_phase3.php and successfully produced static binaries for 4.6.1. Has something changed in the new version? In particular, I am setting: -DCMAKE_SKIP_RPATH=YES -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_C_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops -DCMAKE_CXX_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops but still get dynamic executables: gmx@hector-xe6-5:~/4.6.3-**phase3/bin ldd grompp linux-vdso.so.1 = (0x7fff00da2000) libm.so.6 = /lib64/libm.so.6 (0x7f50dc58f000) libpthread.so.0 = /lib64/libpthread.so.0 (0x7f50dc371000) libAtpSigHandler.so.0 = /opt/cray/lib64/**libAtpSigHandler.so.0 (0x7f50dc16b000) libgfortran.so.3 = /opt/gcc/4.7.2/snos/lib64/**libgfortran.so.3 (0x7f50dbe54000) libscicpp_gnu.so.2 = /opt/cray/lib64/libscicpp_gnu.**so.2 (0x7f50dbc4a000) libsci_gnu_mp.so.2 = /opt/cray/lib64/libsci_gnu_mp.**so.2 (0x7f50d72ec000) libstdc++.so.6 = /opt/gcc/4.7.2/snos/lib64/**libstdc++.so.6 (0x7f50d6fdf000) libfftw3_mpi.so.3 = /opt/cray/lib64/libfftw3_mpi.**so.3 (0x7f50d6dc6000) libfftw3f_mpi.so.3 = /opt/cray/lib64/libfftw3f_mpi.**so.3 (0x7f50d6bae000) libfftw3_threads.so.3 = /opt/cray/lib64/libfftw3_**threads.so.3 (0x7f50d69a6000) libfftw3f_threads.so.3 = /opt/cray/lib64/libfftw3f_**threads.so.3 (0x7f50d679d000) libfftw3.so.3 = /opt/cray/lib64/libfftw3.so.3 (0x7f50d63a2000) libfftw3f.so.3 = /opt/cray/lib64/libfftw3f.so.3 (0x7f50d5f7c000) libmpich_gnu_47.so.1 = /opt/cray/lib64/libmpich_gnu_**47.so.1 (0x7f50d5add000) libmpichf90_gnu_47.so.1 = /opt/cray/lib64/libmpichf90_**gnu_47.so.1 (0x7f50d58da000) libmpl.so.0 = /opt/cray/lib64/libmpl.so.0 (0x7f50d56d5000) librt.so.1 = /lib64/librt.so.1 (0x7f50d54cb000) libxpmem.so.0 = /opt/cray/xpmem/default/lib64/**libxpmem.so.0 (0x7f50d52c9000) libdmapp.so.1 = /opt/cray/dmapp/default/lib64/**libdmapp.so.1 (0x7f50d5092000) libugni.so.0 = /opt/cray/ugni/default/lib64/**libugni.so.0 (0x7f50d4e72000) libpmi.so.0 = /opt/cray/pmi/default/lib64/**libpmi.so.0 (0x7f50d4c51000) libalpslli.so.0 = /usr/lib/alps/libalpslli.so.0 (0x7f50d4a4e000) libalpsutil.so.0 = /usr/lib/alps/libalpsutil.so.0 (0x7f50d4849000) libudreg.so.0 = /opt/cray/udreg/default/lib64/**libudreg.so.0 (0x7f50d4641000) libgomp.so.1 = /opt/gcc/4.7.2/snos/lib64/**libgomp.so.1 (0x7f50d4432000) libc.so.6 = /lib64/libc.so.6 (0x7f50d40d3000) libgcc_s.so.1 = /opt/gcc/4.7.2/snos/lib64/**libgcc_s.so.1 (0x7f50d3ebd000) /lib/ld64.so.1 = /lib64/ld-linux-x86-64.so.2 (0x7f50dc812000) libquadmath.so.0 = /opt/gcc/4.7.2/snos/lib64/**libquadmath.so.0 (0x7f50d3c87000) libcray_memcpy.so.0 = /opt/cray/lib64/libcray_**memcpy.so.0 (0x7f50d3a84000) libopa.so.1 = /opt/cray/lib64/libopa.so.1 (0x7f50d3882000) librca.so.0 =
Re: [gmx-users] GROMACS 4.6.3 Static Linking
That combo is supposed to generate a CMake warning. I also get a warning during linking that some shared library will have to provide some function (getpwuid?) at run time, but the binary is static. Mark On Thu, Jul 25, 2013 at 4:21 PM, Andrew R Turner a.tur...@epcc.ed.ac.uk wrote: Mark, A bit of testing has revealed that it is the -DGMX_PREFER_STATIC_LIBS=ON flag that makes the difference. With this flag you end up with dynamic executables that do not work (I think due to some glibc problem I have not yet tracked down) whereas if I exclude this option then I get working static executables. Thanks for all your help Andy Quoting Mark Abraham mark.j.abra...@gmail.com on Thu, 25 Jul 2013 14:18:35 +0200: Vitaly has it upside down - it is normally required to build a static binary on Crays. cmake .. -DBUILD_SHARED_LIBS=off just works for building static binaries for me with 4.6.3 on lindgren, a Cray XE6, when using PrgEnv-gnu/4.0.46 Mark On Wed, Jul 24, 2013 at 8:58 AM, Andrew R Turner a.tur...@epcc.ed.ac.uk wrote: Hi Vitaly, Impossible just for v4.6.3? It was certainly possible to create static executables for a Cray XE using v4.6.1 (I know, because I have done it). I followed the same procedure for 4.6.3 and have only managed to get dynamic executables (which do not work) hence my question. I will have more of a dig into the build procedure but just wondered if anyone was aware of anything that has changed between these two minor versions (probably in the build process) that could have precipitated this change in behaviour. Cheers Andy Quoting Dr. Vitaly Chaban vvcha...@gmail.com on Sat, 20 Jul 2013 09:42:41 +0200: Soneone said here that static versions are impossible for Cray... Dr. Vitaly V. Chaban On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner a.tur...@epcc.ed.ac.ukwrote: Hi I am having problems creating static versions of the GROMACS binaries for a Cray XE6 (www.hector.ac.uk). The build process I am using is documented at: http://www.hector.ac.uk/**support/documentation/** software/gromacs/compiling_4-**6-1_phase3.phphttp://www.hector.ac.uk/support/documentation/software/gromacs/compiling_4-6-1_phase3.php and successfully produced static binaries for 4.6.1. Has something changed in the new version? In particular, I am setting: -DCMAKE_SKIP_RPATH=YES -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_C_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops -DCMAKE_CXX_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops but still get dynamic executables: gmx@hector-xe6-5:~/4.6.3-**phase3/bin ldd grompp linux-vdso.so.1 = (0x7fff00da2000) libm.so.6 = /lib64/libm.so.6 (0x7f50dc58f000) libpthread.so.0 = /lib64/libpthread.so.0 (0x7f50dc371000) libAtpSigHandler.so.0 = /opt/cray/lib64/**libAtpSigHandler.so.0 (0x7f50dc16b000) libgfortran.so.3 = /opt/gcc/4.7.2/snos/lib64/**libgfortran.so.3 (0x7f50dbe54000) libscicpp_gnu.so.2 = /opt/cray/lib64/libscicpp_gnu.**so.2 (0x7f50dbc4a000) libsci_gnu_mp.so.2 = /opt/cray/lib64/libsci_gnu_mp.**so.2 (0x7f50d72ec000) libstdc++.so.6 = /opt/gcc/4.7.2/snos/lib64/**libstdc++.so.6 (0x7f50d6fdf000) libfftw3_mpi.so.3 = /opt/cray/lib64/libfftw3_mpi.**so.3 (0x7f50d6dc6000) libfftw3f_mpi.so.3 = /opt/cray/lib64/libfftw3f_mpi.**so.3 (0x7f50d6bae000) libfftw3_threads.so.3 = /opt/cray/lib64/libfftw3_**threads.so.3 (0x7f50d69a6000) libfftw3f_threads.so.3 = /opt/cray/lib64/libfftw3f_**threads.so.3 (0x7f50d679d000) libfftw3.so.3 = /opt/cray/lib64/libfftw3.so.3 (0x7f50d63a2000) libfftw3f.so.3 = /opt/cray/lib64/libfftw3f.so.3 (0x7f50d5f7c000) libmpich_gnu_47.so.1 = /opt/cray/lib64/libmpich_gnu_**47.so.1 (0x7f50d5add000) libmpichf90_gnu_47.so.1 = /opt/cray/lib64/libmpichf90_**gnu_47.so.1 (0x7f50d58da000) libmpl.so.0 = /opt/cray/lib64/libmpl.so.0 (0x7f50d56d5000) librt.so.1 = /lib64/librt.so.1 (0x7f50d54cb000) libxpmem.so.0 = /opt/cray/xpmem/default/lib64/**libxpmem.so.0 (0x7f50d52c9000) libdmapp.so.1 = /opt/cray/dmapp/default/lib64/**libdmapp.so.1 (0x7f50d5092000) libugni.so.0 = /opt/cray/ugni/default/lib64/**libugni.so.0 (0x7f50d4e72000) libpmi.so.0 = /opt/cray/pmi/default/lib64/**libpmi.so.0 (0x7f50d4c51000) libalpslli.so.0 = /usr/lib/alps/libalpslli.so.0 (0x7f50d4a4e000) libalpsutil.so.0 = /usr/lib/alps/libalpsutil.so.0 (0x7f50d4849000) libudreg.so.0 = /opt/cray/udreg/default/lib64/**libudreg.so.0 (0x7f50d4641000) libgomp.so.1 = /opt/gcc/4.7.2/snos/lib64/**libgomp.so.1 (0x7f50d4432000) libc.so.6 = /lib64/libc.so.6 (0x7f50d40d3000) libgcc_s.so.1 = /opt/gcc/4.7.2/snos/lib64/**libgcc_s.so.1
[gmx-users] how to set charge 0 in the source code for PME
Dear gmx-users, My system is composed of an ion(CL-) and waters. In the .top file the charge of CL is -1. PME-USER is used to deal with electrostatics. Now I would like set CL charge as 0 in the source code, in order to turn off the ELECTROSTATIC FORCE of Reciprocal part between CL and waters. Anyone has the idea where to change the code? Or, I could set CL charge as 0 in .top file, and PME-USER is still used. Then in the code, how to set CL as -1 in the code for ELECTROSTATIC FORCE of Real part? Yu -- 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] Gromacs on Rescale
Dear users, Please take a moment to check out Gromacs on Rescale. http://blog.rescale.com/run-gromacs-faster-on-rescale-with-parallelization/ We would really appreciate any feedback you might have for us. Best, Joris *Joris Poort* Rescale jo...@rescale.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/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] unable to equilibrate pressure in npt
Dear gromacs users, I know similar issues have been raised many times on the list but I am unable to solve the problem so I am seeking your advice. I am trying to simulate a protein in a dodecahedron box. The system size is ~30k atoms. I have followed the methodology given in the lysozyme tutorial i.e. minimization, nvt, npt and production. However the average pressure values after 5, 10, 20 ns of npt equilibration are not coming close to the reference pressure i.e 1 bar when using parrinello rahman. I checked the mailing list and tried using Berendson and after 10 ns I get average pressure close to 1 (0.85). However when I switch to parrinello rahman for production run the average pressure again goes far from 1. Can someone please help me with this? Here are the g_energy outputs from equilibration (parrinello rahman, 20ns) and production run (10ns after Berendson). Pressure 0.0300644 0.38134.2431.57106 (bar) Pressure -0.0405509 0.79134.204 0.151638 (bar) Can someone please help me with this? Regards. Amin. __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- 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
Aw: [gmx-users] unable to equilibrate pressure in npt
Dear Amin, I did such things in the past, and had similar issues. First of, somone may have beter suggestions. The coupling time will bring it down a bit in the .mdp file (0.2 Vs 2 picoseconds. However, I have found that you will still see large fluctuations around a mean once equilibrated which can vary by 10 to 60, 70 Atomospheres depending on the pressure coupling algorythim used. If it oscillates around this mean, without large up or down changes I assume it is eqd. Basically, if you look at it from the perspective of what pressure itself entails, it is the direct kenetic force of small molecules bumping into each other, so a simple protein movmeent in a small unit cell is turned by the computer into a molar ration, which looks crazy at the macroscopic level, but in reality you do not usually have the unit cell in such a deminsion. This is of course unless your system is made of nothing other than small molecules, which take off a 0 to the oscillation range. the pressure algorythms just keep it from going to insanly large limits, such as an ice cube because of 200 kcal/mol - enthalpy or boiling in the reverse, by pretending there is a universal pressure applied to the unit cell...so a generalized correction for the fact that the unit cell is not really representing infinaty as it is treated by the computer...based on real macroscopic pressures. I may be wrong , but this is my assumption. Stephan Watkins Gesendet:Donnerstag, 25. Juli 2013 um 18:22 Uhr Von:a...@imtech.res.in An:gmx-users@gromacs.org Betreff:[gmx-users] unable to equilibrate pressure in npt Dear gromacs users, I know similar issues have been raised many times on the list but I am unable to solve the problem so I am seeking your advice. I am trying to simulate a protein in a dodecahedron box. The system size is ~30k atoms. I have followed the methodology given in the lysozyme tutorial i.e. minimization, nvt, npt and production. However the average pressure values after 5, 10, 20 ns of npt equilibration are not coming close to the reference pressure i.e 1 bar when using parrinello rahman. I checked the mailing list and tried using Berendson and after 10 ns I get average pressure close to 1 (0.85). However when I switch to parrinello rahman for production run the average pressure again goes far from 1. Can someone please help me with this? Here are the g_energy outputs from equilibration (parrinello rahman, 20ns) and production run (10ns after Berendson). Pressure 0.0300644 0.38 134.243 1.57106 (bar) Pressure -0.0405509 0.79 134.204 0.151638 (bar) Can someone please help me with this? Regards. Amin. __ ( ) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) 39 , / Sector 39-A, Chandigarh /PIN CODE :160036 /EPABX :0172 6665 201-202 -- 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 dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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: gmx-users Digest, Vol 111, Issue 112
Dear Justin, Thanks for your answer... I move so far... My aim was to ask gromacs to read directly a modify protein SOL+NA, not protein SOL NA But I have not succeed so far. Best regards Collins On Wed, Jul 24, 2013 at 8:38 AM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: membrane simulations (Justin Lemkul) 2. interaction energy using g_enemat (Poojari, Chetan) 3. R: Re: [gmx-users] Rotation Constraints - PMF + rerun (battis...@libero.it) 4. Re: OpenSuse 12.1 + CUDA Installation Error (Mirco Wahab) 5. Index error (Collins Nganou) 6. Re: Index error (Justin Lemkul) -- Message: 1 Date: Wed, 24 Jul 2013 07:13:25 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] membrane simulations To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 51efb6d5.2060...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 7/24/13 2:55 AM, Sathish Kumar wrote: I am doing simulation of metal clusters with membranes by position restrain (with f=1000) the membrane. In this simulation the structure of metal cluster is collapsed after entering into membrane. I want to preserves its structure with out doing position restrain the metal cluster because it has to move. Can you please suggest me how can I solve this problem. Geometry is a function of the topology. Setting correct parameters for whatever the desired or expected geometry is should alleviate the issue. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- Message: 2 Date: Wed, 24 Jul 2013 11:47:59 + From: Poojari, Chetan c.pooj...@fz-juelich.de Subject: [gmx-users] interaction energy using g_enemat To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 603fda448cf1c3419be07631a63a3ccf1350c...@mbx2010-k01.ad.fz-juelich.de Content-Type: text/plain; charset=us-ascii Dear All, I want to calculate interaction energy per residue. Below is the command i used: g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm my groups.dat file contains these lines: 3 strand1_SER_34 strand1_THR_36 strand1_TYR_37 When i execute the above g_enemat command i get the below error message: WARNING! could not find group LJ-SR:strand1_SER_34 -strand1_THR_36 (34,36)in energy file WARNING! could not find group Coul-SR:strand1_SER_34 -strand1_TYR_37 (34,37)in energy file My strand.edr file looks like this: LJ-SR:strand1_SER_34-strand1_THR_36 Coul-SR:strand1_SER_34-strand1_TYR_37 Please can I get some suggestions on how to get around this problem. Kind Regards, Chetan Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt Das Forschungszentrum oeffnet seine Tueren am Sonntag, 29. September, von 10:00 bis 17:00 Uhr: http://www.tagderneugier.de -- Message: 3 Date: Wed, 24 Jul 2013 13:59:18 +0200 (CEST) From: battis...@libero.it battis...@libero.it Subject: R: Re: [gmx-users] Rotation Constraints - PMF + rerun To: gmx-users@gromacs.org Message-ID: 1443239804.28991361374667158368.JavaMail.actor@webmail7 Content-Type: text/plain;charset=UTF-8 in my traj.xtc file there are 1 frame every 10 ps from 0 ps to 1 ps, therefore in total 1001 frames. I tried -x trj.xtc instead -o trj.trr, but mdrun has generated a file
[gmx-users] Axis of the box in Gromacs
Hi everybody, I was wondering if you could answer a quick question I had. Where does the axis in a box with PBC lie in Gromacs? I thought 0, 0, 0 was the corner of the box, but if that was true none of the x, y, z values for position should be negative. However in my trajectory I see a value with a negative sign before it which implies the axis might be somewhere else. It seems to happen pretty rarely, so I am not sure why a) more of the values are not in the negative direction or b) why that would happen in this one particular case? -- View this message in context: http://gromacs.5086.x6.nabble.com/Axis-of-the-box-in-Gromacs-tp5010131.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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/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] Axis of the box in Gromacs
If the box is periodic, then it is everywhere. mdrun makes no promises about its output being mapped to a particular box. Mark On Thu, Jul 25, 2013 at 9:56 PM, Neha nshafi...@wesleyan.edu wrote: Hi everybody, I was wondering if you could answer a quick question I had. Where does the axis in a box with PBC lie in Gromacs? I thought 0, 0, 0 was the corner of the box, but if that was true none of the x, y, z values for position should be negative. However in my trajectory I see a value with a negative sign before it which implies the axis might be somewhere else. It seems to happen pretty rarely, so I am not sure why a) more of the values are not in the negative direction or b) why that would happen in this one particular case? -- View this message in context: http://gromacs.5086.x6.nabble.com/Axis-of-the-box-in-Gromacs-tp5010131.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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/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 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] Index error
Please don't reply to the whole digest. On 7/25/13 1:47 PM, Collins Nganou wrote: Dear Justin, Thanks for your answer... I move so far... My aim was to ask gromacs to read directly a modify protein SOL+NA, not protein SOL NA But I have not succeed so far. I don't understand what you're asking here, and without exact commands, output, .mdp settings, etc there's little anyone can do to assist you. Again, the task that you need to carry out is described explicitly in most tutorials so please do make an effort to follow existing protocols. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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] Running GROMACS on mini GPU cluster
On 7/25/13 6:09 PM, Tim Moore wrote: I am running GROMACS 4.6.2 on a GPU cluster in our reasearch group. I am trying to bench mark some systems, and I am getting this message: NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin thread to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). Each node has 2 GTX 580s and 4 physical cores. So when I submit a job I set -nt 2. But since we have a queuing system, there is no way to know which cores will be available to set -pinoffset. Does anyone have a solution, or should I even be worrying about that at all? You're probably not invoking mdrun correctly for your configuration. The wiki page has some useful examples: http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Heterogenous_parallelization.3a_using_GPUs -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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
