Re: [gmx-users] g_energy definition
On 7/23/14, 11:05 PM, Andy Chao wrote: Dear GROMACS USERS: Thanks a lot for your supports and help! I would like to ask more questions related to the output (*.xvg) of the command g_energy. 1. GROMACS computes the potential energy of an ionic liquid to be negative beyond a specific time. What does negative energy of an ionic liquid electrolyte mean? Negative energy means net attraction. 2. What does the calculation of the energy for Bond, Angle, Proper Dih, LJ-14, Coulomb-14, Vir-XY, Pres-YY, etc. represent? Where can I find the reference that explain each term? Most of the terms should be obvious. Bond is the energy of bonds, Angle for angles, etc. The 14 interactions are intramolecular 1-4 interactions. Vir and Pres terms are related to virial and pressure tensors, respectively. 3. I would like to estimate the total free energy of an ionic liquid. How should the total free energy be calculated based on the available selection? You don't. You can get an internal energy and ultimately an enthalpy from the .edr terms, but there is no energy term for entropy; this is true for any MD simulation. There are various ways of calculating entropy in MD simulations, but not from the .edr file. -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: Obtaining Positive Energy Values for Both Potential and Total Energies
Hi, Please leave the discussion on the list. Others may wish to contribute or learn from it! :-) -- Forwarded message -- From: Yip Yew Mun yipy0...@gmail.com Date: Thu, Jul 24, 2014 at 5:16 AM Subject: Re: [gmx-users] Obtaining Positive Energy Values for Both Potential and Total Energies To: mark.j.abra...@gmail.com Hi Mark, Thanks for the prompt reply. I have been trying to obtain the water/octanol partition coefficient of a certain small molecule in TI simulations, in which the result would be compared to the experimental value. That’s the reason why I’m attempting simulations with octanol as the solvent. I have tried topologies from users-contributed gromacs topologies ( http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies http://www.gromacs.org/index.php?title=Download__Installation/User_contributions/Molecule_topologies) as well as from VirtualChemistry. However, since they are described to be equilibrated already, I simply tried to re-run the equilibration to verify it myself. But when I did it, the potential energy values are positive. Therefore, I wish to ask if you know of any sites or in your opinion how should I equilibrate a non-water solvent? It's not fundamentally any different (but see http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation for some clues). If the energies are positive, then either your methodology was wrong (does it work for a water box? for DMSO or something?), or the model is wrong (which is why I suggested the things I already suggested). Mark -- 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] Angle group
I tried using g_angle with an index file defining the three atoms that make up the bond as Group12 ( O1_C1_C4) has 960 elements. I get: Group 0 ( System) has 27396 elements Group 1 ( Other) has 6768 elements Group 2 ( GL4b) has 352 elements Group 3 ( G14b) has 6048 elements Group 4 ( GL1b) has 368 elements Group 5 ( Water) has 20628 elements Group 6 (SOL) has 20628 elements Group 7 ( non-Water) has 6768 elements Group 8 ( O1) has 320 elements Group 9 ( O4) has16 elements Group10 ( C1) has 320 elements Group11 ( C4) has 320 elements Group12 ( O1_C1_C4) has 960 elements Group13 ( C1_O1_C4) has 960 elements Group14 ( C4_C1_O1) has 960 elements Group15 ( C1_C4_O1) has 960 elements Group16 ( O1_C1_C4) has 960 elements Select a group: 12 Selected 12: 'O1_C1_C4' Last frame 1 time 1.000 Found points in the range from 5 to 43 (max 180) angle = 23.1856 angle^2 = 537.601 Std. Dev. = 0.170041 I dont know exactly what angle it is referring to. The angle I'm looking for is formed at the O1-atom, flanked by the carbon atoms and is around 118-120 degrees . As you can see in the index-options I tried defining the triplets in different order, this made no difference however. Any suggestions? Från: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] f#246;r gromacs.org_gmx-users-requ...@maillist.sys.kth.se [gromacs.org_gmx-users-requ...@maillist.sys.kth.se] Skickat: den 23 juli 2014 20:40 Till: gromacs.org_gmx-users@maillist.sys.kth.se Ämne: gromacs.org_gmx-users Digest, Vol 123, Issue 127 Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: Diffusion coefficient of metal complex (Justin Lemkul) 2. Re: Angle group (Justin Lemkul) 3. Re: Error in system_inflate.gro coordinates does not match (RINU KHATTRI) 4. coulomb interactions with zero charge atoms (Sikandar Mashayak) 5. Re: Error in system_inflate.gro coordinates does not match (Justin Lemkul) 6. Lennard-Jones potential not matching with published data (ibrahim khalil) -- Message: 1 Date: Wed, 23 Jul 2014 07:31:13 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Diffusion coefficient of metal complex Message-ID: 53cf9d01.60...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 7/23/14, 7:13 AM, Meena Singh wrote: Dear GROMACS users, I'm working on the diffusivity of metal ion with its ligand in organic phase. I want to calculate the diffusion coefficient of metal-ligand complex as a group, but when I run g_msd command the option are there for only individual molecules diffusivity calculation. Can I calculate the diffusion coefficient of specific complex from the box which contains metal ions and ligand molecules. Does anyone have a suggestion to help me with this problem? Create an index group for whatever subset of atoms you like and use it for the calculation. -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 == -- Message: 2 Date: Wed, 23 Jul 2014 07:30:55 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org, vvcha...@gmail.com Subject: Re: [gmx-users] Angle group Message-ID: 53cf9cef.3070...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 7/23/14, 5:58 AM, Dr. Vitaly Chaban wrote: Use g_angle and your index file must contain triples of the involved atoms. if I remember correctly, this route provides a gaussian-type probability distribution, i.e. not evolution vs. time. The default behavior is to produce a distribution, but g_angle -ov -all will produce individual time series of all the angles in the
[gmx-users] Fw:Normal Mode Analysis
Dear all, I wonder if there is anywhere I can know the details of mdp files used for normal mode analysis. I understand from the maunal that it needs steepest descent, conjugate gradient, l-bfgs, nm in md options consecutively, but I am not sure about other parameters set in these different stages. Many thanks, OAY -- 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] Angle group
On 7/24/14, 8:55 AM, Cyrus Djahedi wrote: I tried using g_angle with an index file defining the three atoms that make up the bond as Group12 ( O1_C1_C4) has 960 elements. I get: Group 0 ( System) has 27396 elements Group 1 ( Other) has 6768 elements Group 2 ( GL4b) has 352 elements Group 3 ( G14b) has 6048 elements Group 4 ( GL1b) has 368 elements Group 5 ( Water) has 20628 elements Group 6 (SOL) has 20628 elements Group 7 ( non-Water) has 6768 elements Group 8 ( O1) has 320 elements Group 9 ( O4) has16 elements Group10 ( C1) has 320 elements Group11 ( C4) has 320 elements Group12 ( O1_C1_C4) has 960 elements Group13 ( C1_O1_C4) has 960 elements Group14 ( C4_C1_O1) has 960 elements Group15 ( C1_C4_O1) has 960 elements Group16 ( O1_C1_C4) has 960 elements Select a group: 12 Selected 12: 'O1_C1_C4' Last frame 1 time 1.000 Found points in the range from 5 to 43 (max 180) angle = 23.1856 angle^2 = 537.601 Std. Dev. = 0.170041 I dont know exactly what angle it is referring to. The angle I'm looking for is formed at the O1-atom, flanked by the carbon atoms and is around 118-120 degrees . As you can see in the index-options I tried defining the triplets in different order, this made no difference however. Any suggestions? The values printed are an average over all triplets in the chosen index group. I would think that order would absolutely matter here; check carefully how you have created the groups. The angle formed by C1-O1-C4 must be different than the angle of O1-C1-C4. -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] continuation run segmentation fault
Dear all
I am having some trouble continuing some runs with Gromacs 4.5.5 in our
local cluster. Surprisingly, the simulations run smoothly in the same
number of nodes and cores before in the same system. And even more
surprisingly if I reduce the number of nodes to 1 with its 12 processors,
then it runs again.
And the script I am using to run the simulations looks something like this@
# Set some Torque options: class name and max time for the job. Torque
developed from a program called
# OpenPBS, hence all the PBS references in this file
#PBS -l nodes=4:ppn=12,walltime=24:00:00
source /home/dd363/src/gromacs-4.5.5/bin/GMXRC.bash
application=/home/user/src/gromacs-4.5.5/bin/mdrun_openmpi_intel
options=-s data/tpr/filename.tpr -deffnm data/filename -cpi data/filename
#! change the working directory (default is home directory)
cd $PBS_O_WORKDIR
echo Running on host `hostname`
echo Time is `date`
echo Directory is `pwd`
echo PBS job ID is $PBS_JOBID
echo This jobs runs on the following machines:
echo `cat $PBS_NODEFILE | uniq`
#! Run the parallel MPI executable
#!export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/lib64:/usr/lib64
echo Running mpiexec $application $options
mpiexec $application $options
And the error messages I am getting look something like this
[compute-0-11:09645] *** Process received signal ***
[compute-0-11:09645] Signal: Segmentation fault (11)
[compute-0-11:09645] Signal code: Address not mapped (1)
[compute-0-11:09645] Failing at address: 0x10
[compute-0-11:09643] *** Process received signal ***
[compute-0-11:09643] Signal: Segmentation fault (11)
[compute-0-11:09643] Signal code: Address not mapped (1)
[compute-0-11:09643] Failing at address: 0xd0
[compute-0-11:09645] [ 0] /lib64/libpthread.so.0 [0x38d300e7c0]
[compute-0-11:09645] [ 1]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_pml_ob1.so
[0x2af2091443f9]
[compute-0-11:09645] [ 2]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_pml_ob1.so
[0x2af209142963]
[compute-0-11:09645] [ 3]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_btl_sm.so
[0x2af20996e33c]
[compute-0-11:09645] [ 4]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libopen-pal.so.0(opal_progress+0x87)
[0x2af20572cfa7]
[compute-0-11:09645] [ 5]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libmpi.so.0
[0x2af205219636]
[compute-0-11:09645] [ 6]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_coll_tuned.so
[0x2af20aa2259b]
[compute-0-11:09645] [ 7]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_coll_tuned.so
[0x2af20aa2a04b]
[compute-0-11:09645] [ 8]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_coll_tuned.so
[0x2af20aa22da9]
[compute-0-11:09645] [ 9]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libmpi.so.0(ompi_comm_split+0xcc)
[0x2af205204dcc]
[compute-0-11:09645] [10]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libmpi.so.0(MPI_Comm_split+0x3c)
[0x2af205236f0c]
[compute-0-11:09645] [11]
/home/dd363/src/gromacs-4.5.5/lib/libgmx_mpi.so.6(gmx_setup_nodecomm+0x14b)
[0x2af204b8ba6b]
[compute-0-11:09645] [12]
/home/dd363/src/gromacs-4.5.5/bin/mdrun_openmpi_intel(mdrunner+0x86c)
[0x415aac]
[compute-0-11:09645] [13]
/home/dd363/src/gromacs-4.5.5/bin/mdrun_openmpi_intel(main+0x1928)
[0x41d968]
[compute-0-11:09645] [14] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x38d281d994]
[compute-0-11:09643] [ 0] /lib64/libpthread.so.0 [0x38d300e7c0]
[compute-0-11:09643] [ 1]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_pml_ob1.so
[0x2b56aca403f9]
[compute-0-11:09643] [ 2]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_pml_ob1.so
[0x2b56aca3e963]
[compute-0-11:09643] [ 3]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_btl_sm.so
[0x2b56ad26a33c]
[compute-0-11:09643] [ 4]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libopen-pal.so.0(opal_progress+0x87)
[0x2b56a9028fa7]
[compute-0-11:09643] [ 5]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libmpi.so.0
[0x2b56a8b15636]
[compute-0-11:09643] [ 6]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_coll_tuned.so
[0x2b56ae31e59b]
[compute-0-11:09643] [ 7]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_coll_tuned.so
[0x2b56ae32604b]
[compute-0-11:09643] [ 8]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_coll_tuned.so
[0x2b56ae31eda9]
[compute-0-11:09643] [ 9]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libmpi.so.0(ompi_comm_split+0xcc)
[0x2b56a8b00dcc]
[compute-0-11:09643] [10]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libmpi.so.0(MPI_Comm_split+0x3c)
[0x2b56a8b32f0c]
[compute-0-11:09643] [11]
Re: [gmx-users] Error in system_inflate.gro coordinates does not match
hello everyone thank you justin i did the same till minimization without the ligand it is in the lipid and center but i edit the box size arbitrary i used x and y axis as present in popc but in z axis used 10.0 so there is overlapping of protein and lipid i think this can create problem help On Wed, Jul 23, 2014 at 10:48 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/23/14, 12:12 PM, RINU KHATTRI wrote: hello everyone thank you justin but how can i increase the box size i am using the box vector which is present in popc_whole.gro how can i edit it editconf and one more problem when i see it in vmd my ligand is out side the protein Position the protein-ligand complex like you want before packing the lipids around the protein, remove the ligand, then assemble the membrane protein system. With strong restraints, the protein should not move, so you can just paste in the ligand coordinates afterwards. Then adjust the box and solvate. -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.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 123, Issue 124: reply to message 1
Thanks for the reply! I actually managed to solve this issue. I was building the super cell with Mercury, the Cambridge Crystallographic Database software, but I was not aware of connectivity issues that appeared when I built the crystal with fragments of molecules. It was solved easily with a different option in the packing/ slicing utility. Thanks! ~ Guilherme * Guilherme D. R. Matos Graduate Student at UC Irvine Mobley Group * On Wed, Jul 23, 2014 at 2:48 AM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: Molecular Solid PBC problem (Justin Lemkul) 2. about cos-accelation (Hyunjin Kim) 3. g_energy questions (Andy Chao) 4. Re: Error in system_inflate.gro coordinates does not match (RINU KHATTRI) 5. Angle group (Cyrus Djahedi) 6. Re: about cos-accelation (Dr. Vitaly Chaban) -- Message: 1 Date: Tue, 22 Jul 2014 20:15:23 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Molecular Solid PBC problem Message-ID: 53cefe9b.4010...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 7/22/14, 7:53 PM, Guilherme Duarte Ramos Matos wrote: Dear GROMACS user community, I'm working with molecular dynamics of molecular solids and I am having trouble to set up the calculations. I got the crystal structure's pdb file from the Cambridge Database and used editconf to generate the coordinate file. The topology file is really simple: it just carries the hamiltonian of an Einstein crystal, that is, harmonic potentials binding each atom of the molecule to its lattice position. The relevant part of the mdp file is: ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 1 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 1.0 Unfortunately, after running grompp, I get the following warning: WARNING 1 [file molecule_ideal.top, line 351]: 10116 non-matching atom names atom names from molecule_ideal.top will be used atom names from input.gro will be ignored The funny and worrying part of this problem is that all the atom types were changed in the output of mdrun. The simulation just didn't crash because of As it should; gromp warned you that a huge number of atoms were out of order with respect to the topology, so the topology is used, and the identity and/or types of the atoms are changed accordingly. the hamiltonian used. I investigated a little bit and it seemed that GROMACS was not able to connect the fragments in the wall to their neighboring periodic copies. That happened because fragments were numbered as distinct molecules. Check this small portion of the coordinate file: How did you generate the original topology? The mismatch between coordinates and topology could also be causing issues with bonded geometry, because everything is likely to get scrambled. 35RES C1 211 0.017 5.561 4.241 35RES N1 212 0.033 5.362 4.363 35RES O1 213 0.145 5.367 4.163 35RES C2 214 0.074 5.421 4.245 35RES H1 215 0.057 5.283 4.386 35RES H3 216 0.087 5.628 4.238 36RES C1 217 0.017 5.561 5.526 36RES N1 218 0.033 5.362 5.648 36RES O1 219 0.145 5.367 5.448 36RES C2 220 0.074 5.421 5.530 36RES H1 221 0.057 5.283 5.671 36RES H3 222 0.087 5.628 5.523 37RES C1 223 0.017 5.561 6.811 37RES N1 224 0.033 5.362 6.933 37RES O1 225 0.145 5.367 6.733 37RES C2 226 0.074 5.421 6.815 37RES H1 227 0.057 5.283 6.956 37RES H3 228 0.087 5.628 6.808 38RES C1 229 0.753 0.786 1.671 38RES N1 230 0.770 0.587 1.793 38RES O1 231 0.882 0.592 1.593 38RES C2 232 0.811 0.646 1.675 38RES O2 233
Re: [gmx-users] Issues using tabulated potentials for coarse-grained simulation
Thanks for the response. I have looked at two particles in NVT with v-rescale/large box and there was nothing wrong with the intra/inter molecular interaction energies. I also switched rvdw-switch to rvdw without observing any difference. I ran into a similar issue when using this force field in a system containing a mixture. I was able to resolve the issue again, though this time with annealing and varying the temperature coupling groups. Perhaps this only happens when there are more degrees of freedom and a greater likelihood for metastability (?). I will just be a bit more cautious from this point on when running these CG simulations. Thanks again, Brian On Wed, Jul 23, 2014 at 4:09 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, All sounds very weird. I would be suspicious of the fact that you haven't set rvdw. I have no idea what rvdw-switch might do in this context, but I definitely think you should verify that systems with just two particles have the interaction strength you can compute manually. Mark On Mon, Jul 21, 2014 at 8:57 PM, Brian Yoo brian.s.yoo...@nd.edu wrote: Dear gmx-users, I am running into an issue regarding the use of tabulated potentials for coarse-grained simulations. My system consists of 256 ion pairs (ionic liquid) and the simulation is run in the NPT ensemble. When I use a temperature coupling on the system as a whole, my system ends up freezing such that the ions vibrate in position. The temperatures and pressures are correct, but the density is much higher than what it should be. Also, the system is stable and the simulation runs indefinitely. However, if I set temperature coupling of anions and cations separately, my molecules no longer freeze and I obtain the targeted properties almost exactly. This occurrence is insensitive to varying tau-t's (0.5 to 5.0) or thermostat (Berendsen or Nose-Hoover), and annealing. It also occurs for other systems using a similar ionic liquid force field, although I was able to resolve the issue again by changing the temperature coupling to anions and cations separately. I have not run into this type of issue for all atom simulations of ionic liquids. The force field is based on a 9-6 Mie cutoff potential and PME long-range electrostatics. Has anyone run into a similar issue using tabulated potentials? Thank you, Brian Yoo The mdp parameters are as follows: integrator = md dt = 0.004 nsteps = 500 comm-mode = linear nstcomm = 1 ; Output control nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstxtcout = 5000 ; Neighbor searching nstlist = 10 ns_type = grid pbc = xyz rlist = 1.5 ;Electrostatics coulombtype = PME rcoulomb= 1.5 fourierspacing = 0.10 optimize_fft= yes ; VdW vdwtype = user rvdw-switch = 1.5 ; Temperature coupling tcoupl = Berendsen tc-grps = C4M PF; System tau_t = 0.5 0.5 ref_t = 300 300 ; Pressure coupling pcoupl = Berendsen pcoupltype = isotropic ref_p = 1.0 tau_p = 3.0 compressibility = 4.5e-5 ; Velocity generation gen_vel = yes continuation= no -- 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. -- 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] Gromacs performance on virtual servers
Dear Gromacs Users, My former university is focusing on cloud computing instead of physical servers, so research groups are now expected to buy virtual servers from the university coloud instead of buying their own clusters. The current setup employs Xeon E7- 2870 servers and there is an university-wide virtual cluster with 50 virtual servers each with 10 CPUs. Does anyone here have information on gromacs performance on this kind of infrastructure? Should I expect big issues? One thing that comes to mind is that the CPUs may not necessarily be in the same physical server, rack, or even datacenter (their plan is to decentralize the colocation), so network latency may be higher than the traditional setup, which may affect scaling. Does this argument make sense or am I missing something on cloud management 101? Cheers. -- Elton Carvalho Departamento de Física Universidade Federal do Paraná -- 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] how to compile and make a C analyzing code under GROMACS 5.0
Dear all, Please help me out. Thanks in advance. I had written some analyzing codes, which can be easily compiled under Gromacs 4.5.5. Since I switched to GMX 5.0 weeks ago, I want to re-compile them under GMX5.0. But the GMX5.0 seems quite different from GMX4.5.5. Anyone can help me? Thanks a lot! I have tried the following methods: 1) (a) save the gmx_density2.c under $HOME/programmes/backup/gromacs-5.0/src/gromacs/gmxana, which is the folder to save all the gmx_XXX.c analyzing codes under the distribution folder; (b) re-install the whole package of GMX5.0 (cmake--make---make install). I got no error message. All regular analyzing programs are correctly installed, but not the gmx_density2! 2) (a) run source $HOME/programmes/GROMACS-5.0/bin/GMXRC; (b) save the gmx_density2.c under $HOME/programmes/GROMACS-5.0/share/gromacs/template, which is under the executable folder; (c) modify the content of CMakeList.txt to change template to gmx_density2, and template.cpp to gmx_density2.c; (d) run cmake .. No error message, and the Makefile and the folder CMakeFiles are created; (e) run make. Then I get the error message gmx_density2.c:42:22: fatal error: sysstuff.h: No such file or directory #include sysstuff.h ^ compilation terminated. make[2]: *** [CMakeFiles/gmx_density2.dir/gmx_density2.c.o] Error 1 make[1]: *** [CMakeFiles/gmx_density2.dir/all] Error 2 make: *** [all] Error 2 best wishes, Baofu -- 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] Issues using tabulated potentials for coarse-grained simulation
Sounds to me like the model is broken, if you can only observe sensible things in the presence of heat to flow between cations and anions via the thermal reservoir. Does NVE work? Mark On Thu, Jul 24, 2014 at 10:27 PM, Brian Yoo brian.s.yoo...@nd.edu wrote: Thanks for the response. I have looked at two particles in NVT with v-rescale/large box and there was nothing wrong with the intra/inter molecular interaction energies. I also switched rvdw-switch to rvdw without observing any difference. I ran into a similar issue when using this force field in a system containing a mixture. I was able to resolve the issue again, though this time with annealing and varying the temperature coupling groups. Perhaps this only happens when there are more degrees of freedom and a greater likelihood for metastability (?). I will just be a bit more cautious from this point on when running these CG simulations. Thanks again, Brian On Wed, Jul 23, 2014 at 4:09 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, All sounds very weird. I would be suspicious of the fact that you haven't set rvdw. I have no idea what rvdw-switch might do in this context, but I definitely think you should verify that systems with just two particles have the interaction strength you can compute manually. Mark On Mon, Jul 21, 2014 at 8:57 PM, Brian Yoo brian.s.yoo...@nd.edu wrote: Dear gmx-users, I am running into an issue regarding the use of tabulated potentials for coarse-grained simulations. My system consists of 256 ion pairs (ionic liquid) and the simulation is run in the NPT ensemble. When I use a temperature coupling on the system as a whole, my system ends up freezing such that the ions vibrate in position. The temperatures and pressures are correct, but the density is much higher than what it should be. Also, the system is stable and the simulation runs indefinitely. However, if I set temperature coupling of anions and cations separately, my molecules no longer freeze and I obtain the targeted properties almost exactly. This occurrence is insensitive to varying tau-t's (0.5 to 5.0) or thermostat (Berendsen or Nose-Hoover), and annealing. It also occurs for other systems using a similar ionic liquid force field, although I was able to resolve the issue again by changing the temperature coupling to anions and cations separately. I have not run into this type of issue for all atom simulations of ionic liquids. The force field is based on a 9-6 Mie cutoff potential and PME long-range electrostatics. Has anyone run into a similar issue using tabulated potentials? Thank you, Brian Yoo The mdp parameters are as follows: integrator = md dt = 0.004 nsteps = 500 comm-mode = linear nstcomm = 1 ; Output control nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstxtcout = 5000 ; Neighbor searching nstlist = 10 ns_type = grid pbc = xyz rlist = 1.5 ;Electrostatics coulombtype = PME rcoulomb= 1.5 fourierspacing = 0.10 optimize_fft= yes ; VdW vdwtype = user rvdw-switch = 1.5 ; Temperature coupling tcoupl = Berendsen tc-grps = C4M PF; System tau_t = 0.5 0.5 ref_t = 300 300 ; Pressure coupling pcoupl = Berendsen pcoupltype = isotropic ref_p = 1.0 tau_p = 3.0 compressibility = 4.5e-5 ; Velocity generation gen_vel = yes continuation= no -- 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. -- 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
[gmx-users] time accounting in log file with GPU
Hi I am running a benchmark test with the GPU. The system consists of simple LJ atoms. And I am running only very basic simulation with NVE ensemble and not writing any trajectories or energy values. My grompp.mdp file is attached below. However, in the time accounting table in the md.log, I observe that write traj. and comm energies operations take 40% of time each. So, my question is that even if I have specified not to write trajectories and energies, why is 80% of time being spent on those operations? Thanks, Sikandar R E A L C Y C L E A N D T I M E A C C O U N T I N G On 2 MPI ranks Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum% - Domain decomp. 21 11 0.006 0.030 2.1 DD comm. load 21 2 0.000 0.000 0.0 Neighbor search21 11 0.007 0.039 2.7 Launch GPU ops.21202 0.007 0.036 2.5 Comm. coord. 21 90 0.002 0.013 0.9 Force 21101 0.001 0.003 0.2 Wait + Comm. F 21101 0.004 0.020 1.4 Wait GPU nonlocal 21101 0.004 0.020 1.4 Wait GPU local 21101 0.000 0.002 0.2 NB X/F buffer ops. 21382 0.001 0.008 0.6 Write traj.21 1 0.108 0.586 40.2 Update 21101 0.005 0.025 1.7 Comm. energies 21 22 0.108 0.588 40.3 Rest 0.016 0.087 5.9 - Total 0.269 1.459 100.0 - grompp.mdp file: integrator = md-vv dt = 0.001 nsteps = 100 nstlog = 0 nstcalcenergy= 0 cutoff-scheme= verlet ns_type = grid nstlist = 10 pbc = xyz rlist= 0.7925 vdwtype = Cut-off rvdw = 0.7925 rcoulomb = 0.7925 gen_vel = yes gen_temp = 296.0 -- 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] how to compile and make a C analyzing code under GROMACS 5.0
On Thu, Jul 24, 2014 at 11:47 PM, qiaobf qia...@gmail.com wrote: Dear all, Please help me out. Thanks in advance. I had written some analyzing codes, which can be easily compiled under Gromacs 4.5.5. Since I switched to GMX 5.0 weeks ago, I want to re-compile them under GMX5.0. But the GMX5.0 seems quite different from GMX4.5.5. Anyone can help me? Thanks a lot! I have tried the following methods: 1) (a) save the gmx_density2.c under $HOME/programmes/backup/ gromacs-5.0/src/gromacs/gmxana, which is the folder to save all the gmx_XXX.c analyzing codes under the distribution folder; (b) re-install the whole package of GMX5.0 (cmake--make---make install). I got no error message. All regular analyzing programs are correctly installed, but not the gmx_density2! That's not too surprising. You had to do more than dump a file into src/tools to get gmx_density2 to build in 4.5.5 ;-) You can probably do something like the above if you register your module with the new gmx binary - see http://jenkins.gromacs.org/job/Doxygen_Gerrit_5_0/javadoc/html-lib/page_wrapperbinary.xhtml 2) (a) run source $HOME/programmes/GROMACS-5.0/bin/GMXRC; (b) save the gmx_density2.c under $HOME/programmes/GROMACS-5.0/share/gromacs/template, which is under the executable folder; (c) modify the content of CMakeList.txt to change template to gmx_density2, and template.cpp to gmx_density2.c; (d) run cmake .. No error message, and the Makefile and the folder CMakeFiles are created; (e) run make. Then I get the error message gmx_density2.c:42:22: fatal error: sysstuff.h: No such file or directory #include sysstuff.h ^ compilation terminated. make[2]: *** [CMakeFiles/gmx_density2.dir/gmx_density2.c.o] Error 1 make[1]: *** [CMakeFiles/gmx_density2.dir/all] Error 2 make: *** [all] Error 2 Things change. You'll need to comment out that #include, see what breaks, and work out how to include the right header to get the right symbols defined. Mark best wishes, Baofu -- 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] continuation run segmentation fault
Hi,
There is a certain version of MPI that caused a lot of headache until
we realized that it is buggy. I'm not entirely sure what version was
it, but I suspect it was the 1.4.3 shipped as default on Ubuntu 12.04
server.
I suggest that you try:
- using a different MPI version;
- using a single rank/no MPI to continue;
- using thread-MPI to continue;
Cheers,
--
Szilárd
On Thu, Jul 24, 2014 at 5:29 PM, David de Sancho
daviddesan...@gmail.com wrote:
Dear all
I am having some trouble continuing some runs with Gromacs 4.5.5 in our
local cluster. Surprisingly, the simulations run smoothly in the same
number of nodes and cores before in the same system. And even more
surprisingly if I reduce the number of nodes to 1 with its 12 processors,
then it runs again.
And the script I am using to run the simulations looks something like this@
# Set some Torque options: class name and max time for the job. Torque
developed from a program called
# OpenPBS, hence all the PBS references in this file
#PBS -l nodes=4:ppn=12,walltime=24:00:00
source /home/dd363/src/gromacs-4.5.5/bin/GMXRC.bash
application=/home/user/src/gromacs-4.5.5/bin/mdrun_openmpi_intel
options=-s data/tpr/filename.tpr -deffnm data/filename -cpi data/filename
#! change the working directory (default is home directory)
cd $PBS_O_WORKDIR
echo Running on host `hostname`
echo Time is `date`
echo Directory is `pwd`
echo PBS job ID is $PBS_JOBID
echo This jobs runs on the following machines:
echo `cat $PBS_NODEFILE | uniq`
#! Run the parallel MPI executable
#!export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/lib64:/usr/lib64
echo Running mpiexec $application $options
mpiexec $application $options
And the error messages I am getting look something like this
[compute-0-11:09645] *** Process received signal ***
[compute-0-11:09645] Signal: Segmentation fault (11)
[compute-0-11:09645] Signal code: Address not mapped (1)
[compute-0-11:09645] Failing at address: 0x10
[compute-0-11:09643] *** Process received signal ***
[compute-0-11:09643] Signal: Segmentation fault (11)
[compute-0-11:09643] Signal code: Address not mapped (1)
[compute-0-11:09643] Failing at address: 0xd0
[compute-0-11:09645] [ 0] /lib64/libpthread.so.0 [0x38d300e7c0]
[compute-0-11:09645] [ 1]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_pml_ob1.so
[0x2af2091443f9]
[compute-0-11:09645] [ 2]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_pml_ob1.so
[0x2af209142963]
[compute-0-11:09645] [ 3]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_btl_sm.so
[0x2af20996e33c]
[compute-0-11:09645] [ 4]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libopen-pal.so.0(opal_progress+0x87)
[0x2af20572cfa7]
[compute-0-11:09645] [ 5]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libmpi.so.0
[0x2af205219636]
[compute-0-11:09645] [ 6]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_coll_tuned.so
[0x2af20aa2259b]
[compute-0-11:09645] [ 7]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_coll_tuned.so
[0x2af20aa2a04b]
[compute-0-11:09645] [ 8]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_coll_tuned.so
[0x2af20aa22da9]
[compute-0-11:09645] [ 9]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libmpi.so.0(ompi_comm_split+0xcc)
[0x2af205204dcc]
[compute-0-11:09645] [10]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libmpi.so.0(MPI_Comm_split+0x3c)
[0x2af205236f0c]
[compute-0-11:09645] [11]
/home/dd363/src/gromacs-4.5.5/lib/libgmx_mpi.so.6(gmx_setup_nodecomm+0x14b)
[0x2af204b8ba6b]
[compute-0-11:09645] [12]
/home/dd363/src/gromacs-4.5.5/bin/mdrun_openmpi_intel(mdrunner+0x86c)
[0x415aac]
[compute-0-11:09645] [13]
/home/dd363/src/gromacs-4.5.5/bin/mdrun_openmpi_intel(main+0x1928)
[0x41d968]
[compute-0-11:09645] [14] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x38d281d994]
[compute-0-11:09643] [ 0] /lib64/libpthread.so.0 [0x38d300e7c0]
[compute-0-11:09643] [ 1]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_pml_ob1.so
[0x2b56aca403f9]
[compute-0-11:09643] [ 2]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_pml_ob1.so
[0x2b56aca3e963]
[compute-0-11:09643] [ 3]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/openmpi/mca_btl_sm.so
[0x2b56ad26a33c]
[compute-0-11:09643] [ 4]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libopen-pal.so.0(opal_progress+0x87)
[0x2b56a9028fa7]
[compute-0-11:09643] [ 5]
/usr/local/shared/redhat-5.4/x86_64/openmpi-1.4.3-intel/lib/libmpi.so.0
[0x2b56a8b15636]
[compute-0-11:09643] [ 6]
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Re: [gmx-users] time accounting in log file with GPU
On Fri, Jul 25, 2014 at 12:12 AM, Sikandar Mashayak symasha...@gmail.com wrote: Hi I am running a benchmark test with the GPU. The system consists of simple LJ atoms. And I am running only very basic simulation with NVE ensemble and not writing any trajectories or energy values. My grompp.mdp file is attached below. However, in the time accounting table in the md.log, I observe that write traj. and comm energies operations take 40% of time each. So, my question is that even if I have specified not to write trajectories and energies, why is 80% of time being spent on those operations? Because you're writing a checkpoint file (hint, use mdrun -noconfout), and that load is imbalanced so the other cores wait for it in the global communication stage in Comm. energies (fairly clear, since they have the same Wall time). Hint - make benchmarks run for about a minute, so you are not dominated by setup and load-balancing time. Your compute time was about 1/20 of a second... Mark Thanks, Sikandar R E A L C Y C L E A N D T I M E A C C O U N T I N G On 2 MPI ranks Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum% - Domain decomp. 21 11 0.006 0.030 2.1 DD comm. load 21 2 0.000 0.000 0.0 Neighbor search21 11 0.007 0.039 2.7 Launch GPU ops.21202 0.007 0.036 2.5 Comm. coord. 21 90 0.002 0.013 0.9 Force 21101 0.001 0.003 0.2 Wait + Comm. F 21101 0.004 0.020 1.4 Wait GPU nonlocal 21101 0.004 0.020 1.4 Wait GPU local 21101 0.000 0.002 0.2 NB X/F buffer ops. 21382 0.001 0.008 0.6 Write traj.21 1 0.108 0.586 40.2 Update 21101 0.005 0.025 1.7 Comm. energies 21 22 0.108 0.588 40.3 Rest 0.016 0.087 5.9 - Total 0.269 1.459 100.0 - grompp.mdp file: integrator = md-vv dt = 0.001 nsteps = 100 nstlog = 0 nstcalcenergy= 0 cutoff-scheme= verlet ns_type = grid nstlist = 10 pbc = xyz rlist= 0.7925 vdwtype = Cut-off rvdw = 0.7925 rcoulomb = 0.7925 gen_vel = yes gen_temp = 296.0 -- 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] Gromacs performance on virtual servers
Hi, Except for huge simulation systems, GROMACS performance past a single node is dominated by network latency, so unless you can extract a promise that any multi-node runs will have Infiniband-quality latency (because the nodes are physically in the same room, and on Infiniband) you can forget about doing multi-node MD on such a system. Mark On Thu, Jul 24, 2014 at 10:54 PM, Elton Carvalho elto...@if.usp.br wrote: Dear Gromacs Users, My former university is focusing on cloud computing instead of physical servers, so research groups are now expected to buy virtual servers from the university coloud instead of buying their own clusters. The current setup employs Xeon E7- 2870 servers and there is an university-wide virtual cluster with 50 virtual servers each with 10 CPUs. Does anyone here have information on gromacs performance on this kind of infrastructure? Should I expect big issues? One thing that comes to mind is that the CPUs may not necessarily be in the same physical server, rack, or even datacenter (their plan is to decentralize the colocation), so network latency may be higher than the traditional setup, which may affect scaling. Does this argument make sense or am I missing something on cloud management 101? Cheers. -- Elton Carvalho Departamento de Física Universidade Federal do Paraná -- 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] time accounting in log file with GPU
Thanks Mark. -noconfout option helps. -- Sikandar On Thu, Jul 24, 2014 at 3:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Fri, Jul 25, 2014 at 12:12 AM, Sikandar Mashayak symasha...@gmail.com wrote: Hi I am running a benchmark test with the GPU. The system consists of simple LJ atoms. And I am running only very basic simulation with NVE ensemble and not writing any trajectories or energy values. My grompp.mdp file is attached below. However, in the time accounting table in the md.log, I observe that write traj. and comm energies operations take 40% of time each. So, my question is that even if I have specified not to write trajectories and energies, why is 80% of time being spent on those operations? Because you're writing a checkpoint file (hint, use mdrun -noconfout), and that load is imbalanced so the other cores wait for it in the global communication stage in Comm. energies (fairly clear, since they have the same Wall time). Hint - make benchmarks run for about a minute, so you are not dominated by setup and load-balancing time. Your compute time was about 1/20 of a second... Mark Thanks, Sikandar R E A L C Y C L E A N D T I M E A C C O U N T I N G On 2 MPI ranks Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum% - Domain decomp. 21 11 0.006 0.030 2.1 DD comm. load 21 2 0.000 0.000 0.0 Neighbor search21 11 0.007 0.039 2.7 Launch GPU ops.21202 0.007 0.036 2.5 Comm. coord. 21 90 0.002 0.013 0.9 Force 21101 0.001 0.003 0.2 Wait + Comm. F 21101 0.004 0.020 1.4 Wait GPU nonlocal 21101 0.004 0.020 1.4 Wait GPU local 21101 0.000 0.002 0.2 NB X/F buffer ops. 21382 0.001 0.008 0.6 Write traj.21 1 0.108 0.586 40.2 Update 21101 0.005 0.025 1.7 Comm. energies 21 22 0.108 0.588 40.3 Rest 0.016 0.087 5.9 - Total 0.269 1.459 100.0 - grompp.mdp file: integrator = md-vv dt = 0.001 nsteps = 100 nstlog = 0 nstcalcenergy= 0 cutoff-scheme= verlet ns_type = grid nstlist = 10 pbc = xyz rlist= 0.7925 vdwtype = Cut-off rvdw = 0.7925 rcoulomb = 0.7925 gen_vel = yes gen_temp = 296.0 -- 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. -- 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] time accounting in log file with GPU
On Fri, Jul 25, 2014 at 12:48 AM, Sikandar Mashayak symasha...@gmail.com wrote: Thanks Mark. -noconfout option helps. For benchmarking purposes, additionally to -noconfout I suggest also using: * -resethway or -resetstep: to exclude initialization and load-balancing at the beginning of the run to get a more realistic performance measurement from a short run * -nsteps N or -maxh: the former is useful if you want to directly compare (e.g. two-sided diff) the timings from the end of the log between multiple runs Cheers, -- Szilárd -- Sikandar On Thu, Jul 24, 2014 at 3:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Fri, Jul 25, 2014 at 12:12 AM, Sikandar Mashayak symasha...@gmail.com wrote: Hi I am running a benchmark test with the GPU. The system consists of simple LJ atoms. And I am running only very basic simulation with NVE ensemble and not writing any trajectories or energy values. My grompp.mdp file is attached below. However, in the time accounting table in the md.log, I observe that write traj. and comm energies operations take 40% of time each. So, my question is that even if I have specified not to write trajectories and energies, why is 80% of time being spent on those operations? Because you're writing a checkpoint file (hint, use mdrun -noconfout), and that load is imbalanced so the other cores wait for it in the global communication stage in Comm. energies (fairly clear, since they have the same Wall time). Hint - make benchmarks run for about a minute, so you are not dominated by setup and load-balancing time. Your compute time was about 1/20 of a second... Mark Thanks, Sikandar R E A L C Y C L E A N D T I M E A C C O U N T I N G On 2 MPI ranks Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum% - Domain decomp. 21 11 0.006 0.030 2.1 DD comm. load 21 2 0.000 0.000 0.0 Neighbor search21 11 0.007 0.039 2.7 Launch GPU ops.21202 0.007 0.036 2.5 Comm. coord. 21 90 0.002 0.013 0.9 Force 21101 0.001 0.003 0.2 Wait + Comm. F 21101 0.004 0.020 1.4 Wait GPU nonlocal 21101 0.004 0.020 1.4 Wait GPU local 21101 0.000 0.002 0.2 NB X/F buffer ops. 21382 0.001 0.008 0.6 Write traj.21 1 0.108 0.586 40.2 Update 21101 0.005 0.025 1.7 Comm. energies 21 22 0.108 0.588 40.3 Rest 0.016 0.087 5.9 - Total 0.269 1.459 100.0 - grompp.mdp file: integrator = md-vv dt = 0.001 nsteps = 100 nstlog = 0 nstcalcenergy= 0 cutoff-scheme= verlet ns_type = grid nstlist = 10 pbc = xyz rlist= 0.7925 vdwtype = Cut-off rvdw = 0.7925 rcoulomb = 0.7925 gen_vel = yes gen_temp = 296.0 -- 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. -- 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
Re: [gmx-users] Gromacs performance on virtual servers
On Fri, Jul 25, 2014 at 1:51 AM, Szilárd Páll pall.szil...@gmail.com wrote: Hi In general, virtualization will always have an overhead, but if done well, the performance should be close to that of bare metal. However, for GROMACS the ideal scenario is exclusive host access (including hypervisor) and thread affinities which will both depend on the hypervisor configuration. Hence, if you can, you should try to get access to virtual hosts that fully utilize a compute node and do not share it with others. On Fri, Jul 25, 2014 at 12:31 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Except for huge simulation systems, GROMACS performance past a single node is dominated by network latency, so unless you can extract a promise that any multi-node runs will have Infiniband-quality latency (because the nodes are physically in the same room, and on Infiniband) you can forget about doing multi-node MD on such a system. Two remarks: * With a slow network the only parallelization you can potentially *inter-node parallelizaion make use of is multi-sim, unless your environment is so could-y that some nodes can have tens to hundreds of ms latency which can kill even you multi-sim performance (depending on how fast each simulation is and how often do they sync). * I've seen several claims that *good* 10/40G Ethernet can get close to IB even in latency, even for MD, and even for GROMACS, e.g: http://goo.gl/JrNxKf, http://goo.gl/t0z15f Cheers, -- Szilárd Mark On Thu, Jul 24, 2014 at 10:54 PM, Elton Carvalho elto...@if.usp.br wrote: Dear Gromacs Users, My former university is focusing on cloud computing instead of physical servers, so research groups are now expected to buy virtual servers from the university coloud instead of buying their own clusters. The current setup employs Xeon E7- 2870 servers and there is an university-wide virtual cluster with 50 virtual servers each with 10 CPUs. Does anyone here have information on gromacs performance on this kind of infrastructure? Should I expect big issues? One thing that comes to mind is that the CPUs may not necessarily be in the same physical server, rack, or even datacenter (their plan is to decentralize the colocation), so network latency may be higher than the traditional setup, which may affect scaling. Does this argument make sense or am I missing something on cloud management 101? Cheers. -- Elton Carvalho Departamento de Física Universidade Federal do Paraná -- 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. -- 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 performance on virtual servers
Hi In general, virtualization will always have an overhead, but if done well, the performance should be close to that of bare metal. However, for GROMACS the ideal scenario is exclusive host access (including hypervisor) and thread affinities which will both depend on the hypervisor configuration. Hence, if you can, you should try to get access to virtual hosts that fully utilize a compute node and do not share it with others. On Fri, Jul 25, 2014 at 12:31 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Except for huge simulation systems, GROMACS performance past a single node is dominated by network latency, so unless you can extract a promise that any multi-node runs will have Infiniband-quality latency (because the nodes are physically in the same room, and on Infiniband) you can forget about doing multi-node MD on such a system. Two remarks: * With a slow network the only parallelization you can potentially make use of is multi-sim, unless your environment is so could-y that some nodes can have tens to hundreds of ms latency which can kill even you multi-sim performance (depending on how fast each simulation is and how often do they sync). * I've seen several claims that *good* 10/40G Ethernet can get close to IB even in latency, even for MD, and even for GROMACS, e.g: http://goo.gl/JrNxKf, http://goo.gl/t0z15f Cheers, -- Szilárd Mark On Thu, Jul 24, 2014 at 10:54 PM, Elton Carvalho elto...@if.usp.br wrote: Dear Gromacs Users, My former university is focusing on cloud computing instead of physical servers, so research groups are now expected to buy virtual servers from the university coloud instead of buying their own clusters. The current setup employs Xeon E7- 2870 servers and there is an university-wide virtual cluster with 50 virtual servers each with 10 CPUs. Does anyone here have information on gromacs performance on this kind of infrastructure? Should I expect big issues? One thing that comes to mind is that the CPUs may not necessarily be in the same physical server, rack, or even datacenter (their plan is to decentralize the colocation), so network latency may be higher than the traditional setup, which may affect scaling. Does this argument make sense or am I missing something on cloud management 101? Cheers. -- Elton Carvalho Departamento de Física Universidade Federal do Paraná -- 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. -- 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] Error in system_inflate.gro coordinates does not match
On 7/24/14, 11:57 AM, RINU KHATTRI wrote: hello everyone thank you justin i did the same till minimization without the ligand it is in the lipid and center but i edit the box size arbitrary i used x and y axis as present in popc but in z axis used 10.0 so there is overlapping of protein and lipid i think this can create problem I don't understand if there is a question or problem here. If something is wrong, provide the exact command(s) used and provide images of the undesirable output. Without that information, there's nothing that I or anyone else can do to help you. -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] Lennard-Jones potential not matching with published data
On 7/24/14, 4:30 PM, Elton Carvalho wrote: On Wed, Jul 23, 2014 at 3:40 PM, ibrahim khalil ibrahim.khalil.c...@gmail.com wrote: In my simulation, my results are about half (not exactly half but around half) of the published data. I am stuck here for like a month and cannot find my mistakes. Can anyone help me where to look for my mistake? I am using a modified oplsaa forcefield. Should i check my forcefield parameters? Or my mdp parameters? I've been there before. Check which Lennard-Jones function was used to publish the data to which you are comparing. There are some nomenclature differences regarding sigma. GROAMCS defines sigma as the distance where the LJ potential is zero. Some forcefields define sigma as the bottom of the well. The definition of sigma is always the same; the issue is whether or not force fields specify sigma directly or Rmin/2, etc. -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] Lennard-Jones potential not matching with published data
On Thu, Jul 24, 2014 at 10:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/24/14, 4:30 PM, Elton Carvalho wrote:
I've been there before.
Check which Lennard-Jones function was used to publish the data to
which you are comparing. There are some nomenclature differences
regarding sigma. GROAMCS defines sigma as the distance where the LJ
potential is zero. Some forcefields define sigma as the bottom of the
well.
The definition of sigma is always the same; the issue is whether or not
force fields specify sigma directly or Rmin/2, etc.
I stand corrected. sigma is well defined. The point is wether the
distance parameter in the LJ formula is sigma or the minimum, or
half the minimum etc. As an example, Accelrys' Cerius2 (and Materials
Studio too, AFIK), define Lennard-Jones as (according to its
documentation):
LJ 12 6: E = Do { ( Ro/R )^12 - 2 * ( Ro/R )^6 }
Do - Well depth in kcal/mol
Ro - Equilibrium distance in Angstroms
This was exactly the scenario I had trouble with: trying to implement
a Cerius2 forcefield in gromacs.
Either way, checking what the distance parameter means in the
forcefield the user is trying to reproduce is a nice to place to start
if he is experiencing this kind of discrepancy.
Cheers from a windy, chilly Curitiba.
--
Elton Carvalho
Departamento de Física
Universidade Federal do Paraná
Departamento de Física
Universidade Federal do Paraná
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[gmx-users] Re grompp and mdrun output files
Hi GROMACS users, I typed the command grompp -f md300.mdp -c equi_new.gro -n dex.ndx -p topol.top -maxwarn 1 -o md300.tpr then this command mdrun -v -deffnm md300 So, I was expecting that the md300.gro output file will be same to the last frame when I load the md300.xtc on the equi_new.gro file on vmd. However, that is not the case. Can anyone please enlighten me about this? Thanks. regards, Melsa -- 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.
