Re: [gmx-users] Continuous mdrun vs step-by-step mdrun
Hi, happy diwali to you, too. Can you please post a link where what you said is stated? it seems quite strange to me! 2012/11/12 Venkat Reddy venkat...@gmail.com Dear gromacs users, I have a very basic doubt regarding mdrun. Is there any difference between doing final MD for 100 ns at a stretch and doing the same with a 10 ns step size (*i.e., 10ns20ns30ns100ns*) on a cluster of 256 processors. I have read some where that continuous MD of longer simulations will cause spurious drifts in velocity and energy, errors in velocity correlationetc. Please advise me in this regard. Thank you and Happy DIWALI -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] do_dssp Segmentation fault
Hello, do_dssp (4.5.5) is broken. There are two possible answers you're gonna get here: 1) Use old dssp, which you are using. 2) You're an idiot, which are not. What I did to solve the problem was, download gmx from git, and substitute the /src/tools/do_dssp.c of gmx 4.5.5 with the one from the git version. Re-compile it and voila! This do_dssp version accepts both old and new dssp and you have to specify which version with the flag -ver if I remember correctly. This worked perfectly for me. I hope it helps you as well. All the best, João Henriques On Mon, Nov 12, 2012 at 8:38 AM, mshappy1986 mshappy1...@126.com wrote: Hi all, I am meeting the following error in Gromacs 4.5.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o dssp.xpm give me the following error segmentation fault I have downloaded the executable DSSP form http://swift.cmbi.ru.nl/gv/dssp/ and set the environment variable, but do_dssp did not work. How can I fix it? Thanks a lot -- 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 -- João Henriques -- 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] Continuous mdrun vs step-by-step mdrun
Hi Francesco, Thanks for ur reply and wishes. I couldn't remember exactly where I read this but what is your opinion on this discrete vs continuous runs ? On Mon, Nov 12, 2012 at 2:10 PM, francesco oteri francesco.ot...@gmail.comwrote: Hi, happy diwali to you, too. Can you please post a link where what you said is stated? it seems quite strange to me! 2012/11/12 Venkat Reddy venkat...@gmail.com Dear gromacs users, I have a very basic doubt regarding mdrun. Is there any difference between doing final MD for 100 ns at a stretch and doing the same with a 10 ns step size (*i.e., 10ns20ns30ns100ns*) on a cluster of 256 processors. I have read some where that continuous MD of longer simulations will cause spurious drifts in velocity and energy, errors in velocity correlationetc. Please advise me in this regard. Thank you and Happy DIWALI -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] About periodic image of system.......
Thank you for your reply. On Sun, Nov 11, 2012 at 8:30 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/11/12 4:51 AM, rama david wrote: Hi justin , Thank you a lot for your explaination. My opinion on the working of g_mindist -pi is that when it shows the distance between two atom of the protein is less than vdw cut off ( 1.4 nm ) , then protein see it periodic image, and it is the violation of pbc. Is these is right??? ( That is the shortest Periodic distance should be larger than vdw cut off 1.4 ) This is correct, when considering a single molecule, i.e. it can't see itself. If you have two proteins, and you choose the blanket Protein group, you haven't determined anything, because now the calculation involves multiple molecules. If it is right, g_mindist say that The shortest periodic distance is 0.154938 (nm) at time 16162 (ps), between atoms 223 and 3270 This is less than 1.4 then Why it is not problem..??? Because they're in separate molecules. Did you ever do as I suggested and visualize this frame? It will be immediately apparent that there is no problem. Please refer to textbooks or even simple Google searching for explanations of the minimum image convention. As I said, it is described in almost every reference text. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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
[gmx-users] About Presence of Water in Hydrophobic core of lipids in NPT equlibration
Dear Justin, Thank you for your previous reply, I am doing Protein-Lipid simulation. After Em When I visualize the str in .vmd The water Molecules Present in Lipid (DPPC) Head groups .There is No Water Molecules Present in the Hydrophobic Part of Bilayer . While The Protein Is in the Center of box . Then I Have done NVT Equilibration When I visualize the .gro file in vmd Around 40 Water molecules (out of 2699 ) are present in Hydrophobic part of Lipid (that is Moving inside the box, Nearer to protein which is at the center) How to Avoid this ? May I simply delete these 40 water Molecules ? or May I freeze these molecules During NVT Equilibration) ? Can i Leave it as such and Then Proceed Further NPT? I Hope Your Valuable Suggestion? Thanks in Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] do_dssp Segmentation fault
Hi, The explanation is that DSSP changed its syntax some time ago and do_dssp no longer complied. More recent versions of do_dssp follows the new syntax while still supporting the old one. Erik 12 nov 2012 kl. 10.55 skrev João Henriques: Hello, do_dssp (4.5.5) is broken. There are two possible answers you're gonna get here: 1) Use old dssp, which you are using. 2) You're an idiot, which are not. What I did to solve the problem was, download gmx from git, and substitute the /src/tools/do_dssp.c of gmx 4.5.5 with the one from the git version. Re-compile it and voila! This do_dssp version accepts both old and new dssp and you have to specify which version with the flag -ver if I remember correctly. This worked perfectly for me. I hope it helps you as well. All the best, João Henriques On Mon, Nov 12, 2012 at 8:38 AM, mshappy1986 mshappy1...@126.com wrote: Hi all, I am meeting the following error in Gromacs 4.5.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o dssp.xpm give me the following error segmentation fault I have downloaded the executable DSSP form http://swift.cmbi.ru.nl/gv/dssp/ and set the environment variable, but do_dssp did not work. How can I fix it? Thanks a lot -- 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 -- João Henriques -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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: Setting up a complex membrane simulation
Ok, what i've currently done: I start with a pdb file of a single molecule Lipid_A and its topology and put it in a box: editconf -f Lipid_A.pdb -o Lipid_A-box.gro -bt triclinic -d 1.0 I want a total of 128 molecules of this lipid in my system so I use genbox to add 127 more: genbox -cp Lipid_A-box.gro -ci Lipid_A.pdb -p Lipid_A.top -o 128_Lipid_A.pdb -nmol 127 This only ads 8 molecules, I'm going to guess because more don't fit in my box. How do I deal with this? How can i know in advance how big i have to make the box? kind regards, -- View this message in context: http://gromacs.5086.n6.nabble.com/Setting-up-a-complex-membrane-simulation-tp5002607p5002885.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] How to launch mdrun_mpi using g_tune_pme on a cluster
Dear Gromacs users, How to launch mdrun_mpi using g_tune_pme on a cluster, because * * *g_tune_pme -launch *launches mdrun but not mdrun_mpi. Thanks for your valuable time -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] How to launch mdrun_mpi using g_tune_pme on a cluster
On 11/12/12 7:40 AM, Venkat Reddy wrote: Dear Gromacs users, How to launch mdrun_mpi using g_tune_pme on a cluster, because * * *g_tune_pme -launch *launches mdrun but not mdrun_mpi. Thanks for your valuable time Please read g_tune_pme -h, which describes how you can set the names of mpirun and mdrun executables. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] About Presence of Water in Hydrophobic core of lipids in NPT equlibration
On 11/12/12 6:35 AM, vidhya sankar wrote: Dear Justin, Thank you for your previous reply, I am doing Protein-Lipid simulation. After Em When I visualize the str in .vmd The water Molecules Present in Lipid (DPPC) Head groups .There is No Water Molecules Present in the Hydrophobic Part of Bilayer . While The Protein Is in the Center of box . Then I Have done NVT Equilibration When I visualize the .gro file in vmd Around 40 Water molecules (out of 2699 ) are present in Hydrophobic part of Lipid (that is Moving inside the box, Nearer to protein which is at the center) How to Avoid this ? Some water will diffuse into the lipid headgroup and ester regions, which are largely devoid of water based on the method of increasing the van der Waals radius of carbon, but will normally be hydrated. If the water molecules are diffusing all the way into the membrane, making contact with the lipid tails themselves, this would be very odd and I suspect a result of incorrect packing of the lipids. That's a blind guess, and I'm not going to try to predict what's going on in your system, but it would be very odd for a properly equilibrated membrane to allow that many water molecules to diffuse deeply within it. May I simply delete these 40 water Molecules ? or Maybe. May I freeze these molecules During NVT Equilibration) ? The better approach would be a position restrain along the z-axis only, allowing the lipids to perhaps re-orient and pack a bit better, followed by NVT equilibration in the absence of any restraints on water. Can i Leave it as such and Then Proceed Further NPT? You could, but expect your equilibration to last significantly longer than normal for the hydrophobic effect to expel any water molecules that are in bad places. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] Re: Setting up a complex membrane simulation
On 11/12/12 7:03 AM, jonas87 wrote: Ok, what i've currently done: I start with a pdb file of a single molecule Lipid_A and its topology and put it in a box: editconf -f Lipid_A.pdb -o Lipid_A-box.gro -bt triclinic -d 1.0 I want a total of 128 molecules of this lipid in my system so I use genbox to add 127 more: genbox -cp Lipid_A-box.gro -ci Lipid_A.pdb -p Lipid_A.top -o 128_Lipid_A.pdb -nmol 127 This only ads 8 molecules, I'm going to guess because more don't fit in my box. How do I deal with this? How can i know in advance how big i have to make the box? You would need to know the volume of an individual lipid in the configuration that you are supplying, plus a volume that will allow for any other species in the system (like water) to yield the desired composition of the system. The above series of commands yields a very small box, as you have found. Most 128-lipid membranes are on the order of 6-8 nm cubes, depending on the specific properties of the lipids being studied. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 4.6 segmentation fault with mdrun
Dear GROMACS user, I am running in major problems trying to use gromacs 4.6 on my desktop with two GTX 670 GPU's and one i7 cpu. On the system I installed the CUDA 4.2, running fine for many different test programs. Compiling the git version of gromacs 4.6 with hybrid acceleration I get one error message of a missing libxml2 but it compiles with no further complaints. The tools I tested (like g_rdf or grompp usw.) work fine as long as I generate the tpr files with the right gromacs version. Now, if I try to use mdrun (GMX_GPU_ID=1 mdrun -nt 1 -v -deffnm ) the preparation seems to work fine until it starts the actual run. It stops with a segmentation fault: Reading file pdz_cis_ex_200ns_test.tpr, VERSION 4.6-dev-20121002-20da718-dirty (single precision) Using 1 MPI thread Using 1 OpenMP thread 2 GPUs detected: #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU user-selected to be used for this run: #1 Using CUDA 8x8x8 non-bonded kernels * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING * We have just committed the new CPU detection code in this branch, and will commit new SSE/AVX kernels in a few days. However, this means that currently only the NxN kernels are accelerated! In the mean time, you might want to avoid production runs in 4.6. Back Off! I just backed up pdz_cis_ex_200ns_test.trr to ./#pdz_cis_ex_200ns_test.trr.4# Back Off! I just backed up pdz_cis_ex_200ns_test.xtc to ./#pdz_cis_ex_200ns_test.xtc.4# Back Off! I just backed up pdz_cis_ex_200ns_test.edr to ./#pdz_cis_ex_200ns_test.edr.4# starting mdrun 'Protein in water' 350 steps, 7000.0 ps. Segmentation fault Since I have no idea whats going wrong any help is welcomed. Attached you find the log file. Thanks a lot Sebastian -- 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] is it possible?
Hello: Recently, in a released paper I found that some one claimed they've observed a Asp is protonated and deprotonated from time to time during a micro second MD simulation by Gromacs. I am still curious about such kind of observation. Does anybody else observe a covalent bond can be broken in normal MD simulations? thank you very much Albert -- 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] Error of violate the Second Law of Thermodynamics in Free energy calculation with BAR
Dear GMX users Hi. I'm calculating some small organic molecule's desolvation free energy. Recently i got this error from BAR calculation. Please anyone explain what's wrong in here? First: WARNING: Using the derivative data (dH/dlambda) to extrapolate delta H values. This will only work if the Hamiltonian is linear in lambda. and then Second: WARNING: Some of these results violate the Second Law of Thermodynamics: This is can be the result of severe undersampling, or (more likely) there is something wrong with the simulations. I have two MD simulation steps. For example desolvation free energy of chloroform and methanol: The final result from MD1 something like this: total 0.000 - 1.000, DG 7.72 +/- 0.05 The final result from MD2 something like this: total 0.000 - 1.000, DG 3.96 +/- 0.06 Total Gibbs energy of desolvation 11.7 +/- 0.1 kJ/mol (including with these two warnings) Something wrong in MD? MD1.mdp ;Run control integrator = sd ; Langevin dynamics tinit = 0 dt = 0.002 nsteps = 100 ; 2 ns nstcomm = 100 ; Output control nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy = 500 nstxtcout = 0 xtc-precision = 1000 ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 ; Electrostatics coulombtype = PME rcoulomb = 1.0 ; van der Waals vdw-type = switch rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc_grps = system tau_t = 0.2 ref_t = 300 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman tau_p = 5 compressibility = 4.5e-05 ref_p = 1.0 ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-lambda0 = vdw-q ; only van der Waals interactions couple-lambda1 = vdw ; turn off everything, in this case only vdW couple-intramol = no nstdhdl = 10 ; Do not generate velocities gen_vel = no ; options for bonds constraints = all-bonds ; ; Type of constraint algorithm constraint-algorithm = lincs ; Constrain the starting configuration ; since we are continuing from NPT continuation = yes ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 MD2.mdp ;Run control integrator = sd ; Langevin dynamics tinit = 0 dt = 0.002 nsteps = 100 ; 2 ns nstcomm = 100 ; Output control nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy = 500 nstxtcout = 0 xtc-precision = 1000 ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 ; Electrostatics coulombtype = PME rcoulomb = 1.0 ; van der Waals vdw-type = switch rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc_grps = system tau_t = 0.2 ref_t = 300 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman tau_p = 5 compressibility = 4.5e-05 ref_p = 1.0 ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma
[gmx-users] Question about scaling
Dear all, i did some scaling tests for a cluster and i'm a little bit clueless about the results. So first the setup: Cluster: Saxonid 6100, Opteron 6272 16C 2.100GHz, Infiniband QDR GROMACS version: 4.0.7 and 4.5.5 Compiler: GCC 4.7.0 MPI: Intel MPI 4.0.3.008 FFT-library: ACML 5.1.0 fma4 System: 895 spce water molecules Simulation time: 750 ps (0.002 fs timestep) Cut-off: 1.0 nm but with long-range correction ( DispCorr = EnerPres ; PME (standard settings) - but in each case no extra CPU solely for PME) V-rescale thermostat and Parrinello-Rahman barostat I get the following timings (seconds), whereas is calculated as the time which would be needed for 1 CPU (so if a job on 2 CPUs took X s the time would be 2 * X s). These timings were taken from the *.log file, at the end of the 'real cycle and time accounting' - section. Timings: gmx-version 1cpu2cpu4cpu 4.0.7 422333843540 4.5.5 378032552878 I'm a little bit clueless about the results. I always thought, that if i have a non-interacting system and double the amount of CPUs, i would get a simulation which takes only half the time (so the times as defined above would be equal). If the system does have interactions, i would lose some performance due to communication. Due to node imbalance there could be a further loss of performance. Keeping this in mind, i can only explain the timings for version 4.0.7 2cpu - 4cpu (2cpu a little bit faster, since going to 4cpu leads to more communication - loss of performance). All the other timings, especially that 1cpu takes in each case longer than the other cases, i do not understand. Probalby the system is too small and / or the simulation time is too short for a scaling test. But i would assume that the amount of time to setup the simulation would be equal for all three cases of one GROMACS-version. Only other explaination, which comes to my mind, would be that something went wrong during the installation of the programs... Please, can somebody enlighten me? Greetings Thomas -- 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] is it possible?
On 11/12/12 10:29 AM, Albert wrote: Hello: Recently, in a released paper I found that some one claimed they've observed a Asp is protonated and deprotonated from time to time during a micro second MD simulation by Gromacs. I am still curious about such kind of observation. Does anybody else observe a covalent bond can be broken in normal MD simulations? A link to the paper would be helpful, otherwise the commentary is a bit vague. In classical MD, no, bonds cannot break and form, but there are ways of changing protonation states (titration MD, dual-topology approaches with virtual sites, etc). Titration MD is in the works for Gromacs, but at present, is not possible. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] Question about scaling
Hi Thomas, On Nov 12, 2012, at 5:18 PM, Thomas Schlesier schl...@uni-mainz.de wrote: Dear all, i did some scaling tests for a cluster and i'm a little bit clueless about the results. So first the setup: Cluster: Saxonid 6100, Opteron 6272 16C 2.100GHz, Infiniband QDR GROMACS version: 4.0.7 and 4.5.5 Compiler: GCC 4.7.0 MPI: Intel MPI 4.0.3.008 FFT-library: ACML 5.1.0 fma4 System: 895 spce water molecules this is a somewhat small system I would say. Simulation time: 750 ps (0.002 fs timestep) Cut-off: 1.0 nm but with long-range correction ( DispCorr = EnerPres ; PME (standard settings) - but in each case no extra CPU solely for PME) V-rescale thermostat and Parrinello-Rahman barostat I get the following timings (seconds), whereas is calculated as the time which would be needed for 1 CPU (so if a job on 2 CPUs took X s the time would be 2 * X s). These timings were taken from the *.log file, at the end of the 'real cycle and time accounting' - section. Timings: gmx-version 1cpu2cpu4cpu 4.0.7 422333843540 4.5.5 378032552878 Do you mean CPUs or CPU cores? Are you using the IB network or are you running single-node? I'm a little bit clueless about the results. I always thought, that if i have a non-interacting system and double the amount of CPUs, i You do use PME, which means a global interaction of all charges. would get a simulation which takes only half the time (so the times as defined above would be equal). If the system does have interactions, i would lose some performance due to communication. Due to node imbalance there could be a further loss of performance. Keeping this in mind, i can only explain the timings for version 4.0.7 2cpu - 4cpu (2cpu a little bit faster, since going to 4cpu leads to more communication - loss of performance). All the other timings, especially that 1cpu takes in each case longer than the other cases, i do not understand. Probalby the system is too small and / or the simulation time is too short for a scaling test. But i would assume that the amount of time to setup the simulation would be equal for all three cases of one GROMACS-version. Only other explaination, which comes to my mind, would be that something went wrong during the installation of the programs… You might want to take a closer look at the timings in the md.log output files, this will give you a clue where the bottleneck is, and also tell you about the communication-computation ratio. Best, Carsten Please, can somebody enlighten me? Greetings Thomas -- 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 -- 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 segmentation fault with mdrun
On 11/12/2012 04:12 PM, sebastian wrote: Dear GROMACS user, I am running in major problems trying to use gromacs 4.6 on my desktop with two GTX 670 GPU's and one i7 cpu. On the system I installed the CUDA 4.2, running fine for many different test programs. Compiling the git version of gromacs 4.6 with hybrid acceleration I get one error message of a missing libxml2 but it compiles with no further complaints. The tools I tested (like g_rdf or grompp usw.) work fine as long as I generate the tpr files with the right gromacs version. Now, if I try to use mdrun (GMX_GPU_ID=1 mdrun -nt 1 -v -deffnm ) the preparation seems to work fine until it starts the actual run. It stops with a segmentation fault: Reading file pdz_cis_ex_200ns_test.tpr, VERSION 4.6-dev-20121002-20da718-dirty (single precision) Using 1 MPI thread Using 1 OpenMP thread 2 GPUs detected: #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU user-selected to be used for this run: #1 Using CUDA 8x8x8 non-bonded kernels * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING * We have just committed the new CPU detection code in this branch, and will commit new SSE/AVX kernels in a few days. However, this means that currently only the NxN kernels are accelerated! Since it does run on a pure CPU run (without the verlet cut-off scheme) does it maybe help to change the NxN kernels manually in the .mdp file (how can I do so)? Or is there something wrong using the CUDA 4.2 version or what so ever. The libxml2 should not be a problem since the pure CPU run works. In the mean time, you might want to avoid production runs in 4.6. Back Off! I just backed up pdz_cis_ex_200ns_test.trr to ./#pdz_cis_ex_200ns_test.trr.4# Back Off! I just backed up pdz_cis_ex_200ns_test.xtc to ./#pdz_cis_ex_200ns_test.xtc.4# Back Off! I just backed up pdz_cis_ex_200ns_test.edr to ./#pdz_cis_ex_200ns_test.edr.4# starting mdrun 'Protein in water' 350 steps, 7000.0 ps. Segmentation fault Since I have no idea whats going wrong any help is welcomed. Attached you find the log file. Help is really appreciated since I want to use my new desktop including the GPU's Thanks a lot Sebastian -- 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] compressibility water - TFE mixture
Dear Users, I would like to study water - TFE mixtures at different molar ratios. Is it a reasonably approach to set the compressibility to the value of water at [100/0 - water/TFE] and to that of tfe at [0/100 - water/TFE] and scale the compressibility values for the other mixtures? Thnak you for your help in advance! Balazs -- 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 segmentation fault with mdrun
Hi Sebastian, That is very likely a bug so I'd appreciate if you could provide a bit more information, like: - OS, compiler - results of runs with the following configurations: - mdrun -nb cpu (to run CPU-only with Verlet scheme) - GMX_EMULATE_GPU=1 mdrun -nb gpu (to run GPU emulation using plain C kernels); - mdrun without any arguments (which will use 2x(n/2 cores + 1 GPU)) - mdrun -ntmpi 1 without any other arguments (which will use n cores + the first GPU) - please attach the log files of all failed and a successful run as well as the mdrun.debug file from a failed runs that you can obtain with mdrun -debug 1 Note that a backtrace would be very useful and if you can get one I'd be grateful, but for now the above should be minimum effort and I'll provide simple introductions to get a backtrace later (if needed). Thanks, -- Szilárd On Mon, Nov 12, 2012 at 6:22 PM, sebastian sebastian.wa...@physik.uni-freiburg.de wrote: On 11/12/2012 04:12 PM, sebastian wrote: Dear GROMACS user, I am running in major problems trying to use gromacs 4.6 on my desktop with two GTX 670 GPU's and one i7 cpu. On the system I installed the CUDA 4.2, running fine for many different test programs. Compiling the git version of gromacs 4.6 with hybrid acceleration I get one error message of a missing libxml2 but it compiles with no further complaints. The tools I tested (like g_rdf or grompp usw.) work fine as long as I generate the tpr files with the right gromacs version. Now, if I try to use mdrun (GMX_GPU_ID=1 mdrun -nt 1 -v -deffnm ) the preparation seems to work fine until it starts the actual run. It stops with a segmentation fault: Reading file pdz_cis_ex_200ns_test.tpr, VERSION 4.6-dev-20121002-20da718-dirty (single precision) Using 1 MPI thread Using 1 OpenMP thread 2 GPUs detected: #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU user-selected to be used for this run: #1 Using CUDA 8x8x8 non-bonded kernels * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING * We have just committed the new CPU detection code in this branch, and will commit new SSE/AVX kernels in a few days. However, this means that currently only the NxN kernels are accelerated! Since it does run on a pure CPU run (without the verlet cut-off scheme) does it maybe help to change the NxN kernels manually in the .mdp file (how can I do so)? Or is there something wrong using the CUDA 4.2 version or what so ever. The libxml2 should not be a problem since the pure CPU run works. In the mean time, you might want to avoid production runs in 4.6. Back Off! I just backed up pdz_cis_ex_200ns_test.trr to ./#pdz_cis_ex_200ns_test.trr.4# Back Off! I just backed up pdz_cis_ex_200ns_test.xtc to ./#pdz_cis_ex_200ns_test.xtc.4# Back Off! I just backed up pdz_cis_ex_200ns_test.edr to ./#pdz_cis_ex_200ns_test.edr.4# starting mdrun 'Protein in water' 350 steps, 7000.0 ps. Segmentation fault Since I have no idea whats going wrong any help is welcomed. Attached you find the log file. Help is really appreciated since I want to use my new desktop including the GPU's Thanks a lot Sebastian -- 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
[gmx-users] Re: Setting up a complex membrane simulation
The simple answer is yes, you could make Lipid_A-box.gro larger in the bilayer plane. That probably won`t address the underlying problem though. As far as I know, genbox doesn't take periodicity into account. That means that with larger species, such as lipid A you are going to need to start with a much larger box and let pressure equilibration bring it down to the correct size in the context of PBC during mdrun. The alternative is to build a crystal with your own script and then set the box boundaries yourself so that periodicity is taken into account. Note that this is a major limitation of genbox and it would be great if somebody had the time to address it... Also note that there will be a similar packing problem between lipids even if you discount problems with PBC packing. There are only 2 ways to deal with this: (a) start with a crystal or (b) start with a sparse bilayer and have a good equilibration technique. If you go for option A then you need to be aware of biases from the starting crystal. If you go for option B, then you'll likely have problems with lipid A acyl chains moving out toward bulk water and then not equilibrating on your achievable simulation timescale (there's at least one paper out there describing how to build a lipid A system and circumvent some setup problems, you should read it. I think it's at least 10 years old). The main problem with setup is that lipid A equilibration times are orders of magnitude larger than those for phospholipids. I have personally had good success with high-temperature equilibration in which I add restraints to a number of atoms that keep their z-coordinates in certain regions (where z is along the bilayer normal). In fact, a good technique is probably to build a sparse lipid A bilayer, restrain all Z coordinates of all lipid A atoms to their original values, and run some high-temperature MD to get some preliminary packing before slowly releasing the z-value restraints. I haven`t done this myself, but it is what I would do the next time I need to build a lipid A bilayer from scratch. Finally, there are papers recently in the literature of lipid A simulations. Perhaps you can get a lipid A bilayer from one of those groups. I didn't have any luck obtaining these myself but perhaps they will be kinder to you if you ask nicely. Then you can bypass the building step entirely. Chris. -- original message -- Ok, what i've currently done: I start with a pdb file of a single molecule Lipid_A and its topology and put it in a box: editconf -f Lipid_A.pdb -o Lipid_A-box.gro -bt triclinic -d 1.0 I want a total of 128 molecules of this lipid in my system so I use genbox to add 127 more: genbox -cp Lipid_A-box.gro -ci Lipid_A.pdb -p Lipid_A.top -o 128_Lipid_A.pdb -nmol 127 This only ads 8 molecules, I'm going to guess because more don't fit in my box. How do I deal with this? How can i know in advance how big i have to make the box? kind regards, -- 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
