Re: [gmx-users] regarding MSD
Hello I have posted the query earlier but havent got any reply and so reposting it again. I have read few papers that determine transition temperature from the plot of average MSD of hydrogen atoms of protein versus temperature. My question is: At a particular temperature, we get a linear curve for MSD versus time, is it reasonable to calculate average MSD over all such time points? Is this the average that is plotted in papers (or something is missing) ? My doubt is won't this average depend on the number of time points (due to its linear nature)? Actually I am trying to reproduce the results of some published data. Although I am getting the same transition temperature but the MSD values are coming different (eg at a particular temperature if I average all the MSD values, I am getting value of 15000 while reported value is 1.5 - both values in same unit angstrom square) Any help is highly appreciated. On Thu, Aug 21, 2014 at 9:56 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Hello all I have read few papers that determine transition temperature from the plot of average MSD versus temperature. My question is: At a particular temperature, we get a linear curve for MSD versus time, is it reasonable to calculate average MSD over all such time points? Is this the average that is plotted in papers (or something is missing) ? My doubt is won't this average depend on the number of time points (due to its linear nature)? Any help is highly appreciated. Thanks Nidhi -- 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] Why we are not using GPU to solve FFT?
Hi, I wonder why we are using cpu instead of gpu to solve FFT? Is it possible to use gpu fft library, say cuFFT to make the FFT used in PME faster? BR, Theo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] regarding g_hydorder
Hello all I would like to calculate both distance and angle water orientational order. I have made an index file containing all oxygen atoms of water and used trjorder as: g_hydorder -f *.xtc -s *.tpr -n *.ndx -o file1_1 file2_1 -or file1_2 file2_2 How to interpret the results of the output files? Both output files file1_2 and file2_2 contain the same content. Won't one should contain distance and other angle orientational order parameter values? Also I expect parameter values to be less than or equal to 1. But the values in the file looks something like the following (all greater than 1): #Legend #TBlock #Xbin Ybin Z t 0 0 0 6.5 0 1 6.5 0 2 4.5 0 3 3.5 0 4 6.5 0 5 4.5 0 6 5.5 1 0 6.5 1 1 4.5 1 2 5.5 1 3 3.5 1 4 5.5 1 5 4.5 1 6 5.5 2 0 4.5 . . Please help me in interpreting this file. Thanks Nidhi -- 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] Why we are not using GPU to solve FFT?
On Fri, Aug 22, 2014 at 9:10 AM, Theodore Si sjyz...@gmail.com wrote: Hi, I wonder why we are using cpu instead of gpu to solve FFT? While people continue to attach GPUs to nodes with tasty x86 cores, we'd like to use them. Adding more work to the GPU while leaving the CPU idle does not improve throughput. Is it possible to use gpu fft library, say cuFFT to make the FFT used in PME faster? Perhaps, on a single node, if someone were to write the code to do it. But on mutliple nodes on current-generation hardware, a 3DFFT that has to do data transfer, kernel launch and then go back across PCI to get to Infiniband to do the all-to-all would be horrendous. The latency of all-to-all communication already limits scaling without, say, doubling the length of that latency. Mark BR, Theo -- 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] Can we set the number of pure PME nodes when using GPUCPU?
Hi Mark, Could you tell me why that when we are GPU-CPU nodes as PME-dedicated nodes, the GPU on such nodes will be idle? Theo On 8/11/2014 9:36 PM, Mark Abraham wrote: Hi, What Carsten said, if running on nodes that have GPUs. If running on a mixed setup (some nodes with GPU, some not), then arranging your MPI environment to place PME ranks on CPU-only nodes is probably worthwhile. For example, all your PP ranks first, mapped to GPU nodes, then all your PME ranks, mapped to CPU-only nodes, and then use mdrun -ddorder pp_pme. Mark On Mon, Aug 11, 2014 at 2:45 AM, Theodore Si sjyz...@gmail.com wrote: Hi Mark, This is information of our cluster, could you give us some advice as regards to our cluster so that we can make GMX run faster on our system? Each CPU node has 2 CPUs and each GPU node has 2 CPUs and 2 Nvidia K20M Device Name Device Type Specifications Number CPU NodeIntelH2216JFFKRNodesCPU: 2×Intel Xeon E5-2670(8 Cores, 2.6GHz, 20MB Cache, 8.0GT) Mem: 64GB(8×8GB) ECC Registered DDR3 1600MHz Samsung Memory 332 Fat NodeIntelH2216WPFKRNodesCPU: 2×Intel Xeon E5-2670(8 Cores, 2.6GHz, 20MB Cache, 8.0GT) Mem: 256G(16×16G) ECC Registered DDR3 1600MHz Samsung Memory20 GPU NodeIntelR2208GZ4GC CPU: 2×Intel Xeon E5-2670(8 Cores, 2.6GHz, 20MB Cache, 8.0GT) Mem: 64GB(8×8GB) ECC Registered DDR3 1600MHz Samsung Memory 50 MIC NodeIntelR2208GZ4GC CPU: 2×Intel Xeon E5-2670(8 Cores, 2.6GHz, 20MB Cache, 8.0GT) Mem: 64GB(8×8GB) ECC Registered DDR3 1600MHz Samsung Memory 5 Computing Network SwitchMellanox Infiniband FDR Core Switch 648× FDR Core Switch MSX6536-10R, Mellanox Unified Fabric Manager 1 Mellanox SX1036 40Gb Switch 36× 40Gb Ethernet Switch SX1036, 36× QSFP Interface 1 Management Network Switch Extreme Summit X440-48t-10G 2-layer Switch 48× 1Giga Switch Summit X440-48t-10G, authorized by ExtremeXOS 9 Extreme Summit X650-24X 3-layer Switch 24× 10Giga 3-layer Ethernet Switch Summit X650-24X, authorized by ExtremeXOS1 Parallel StorageDDN Parallel Storage System DDN SFA12K Storage System 1 GPU GPU Accelerator NVIDIA Tesla Kepler K20M70 MIC MIC Intel Xeon Phi 5110P Knights Corner 10 40Gb Ethernet Card MCX314A-BCBTMellanox ConnextX-3 Chip 40Gb Ethernet Card 2× 40Gb Ethernet ports, enough QSFP cables 16 SSD Intel SSD910Intel SSD910 Disk, 400GB, PCIE 80 On 8/10/2014 5:50 AM, Mark Abraham wrote: That's not what I said You can set... -npme behaves the same whether or not GPUs are in use. Using separate ranks for PME caters to trying to minimize the cost of the all-to-all communication of the 3DFFT. That's still relevant when using GPUs, but if separate PME ranks are used, any GPUs on nodes that only have PME ranks are left idle. The most effective approach depends critically on the hardware and simulation setup, and whether you pay money for your hardware. Mark On Sat, Aug 9, 2014 at 2:56 AM, Theodore Si sjyz...@gmail.com wrote: Hi, You mean no matter we use GPU acceleration or not, -npme is just a reference? Why we can't set that to a exact value? On 8/9/2014 5:14 AM, Mark Abraham wrote: You can set the number of PME-only ranks with -npme. Whether it's useful is another matter :-) The CPU-based PME offload and the GPU-based PP offload do not combine very well. Mark On Fri, Aug 8, 2014 at 7:24 AM, Theodore Si sjyz...@gmail.com wrote: Hi, Can we set the number manually with -npme when using GPU acceleration? -- 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 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
[gmx-users] (no subject)
Dear Users, generally for running a 10 ns simulation is there any online server facility available. This will be helpful for people who do not have a continuous access to the server. regards Suriyanarayanan -- 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] ligand is out side the box
hello gromacs users i am working on protein ligand complex with POPC membrane according to justin (from previous mail) i built the system without ligand and after minimization and shrink paste the ligand and edit the box size but after solvation and water addition ligand is out side the box grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname CL -nn 14 grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em you can see the image i have been uploaded kindly help http://s48.photobucket.com/user/mittukhattri/media/pic_zpse022cdb3.png.html?filters[user]=140927090filters[recent]=1sort=1o=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.
[gmx-users] pme ranks
Does anyone know that what the pme ranks mean? xiexiao...@sjtu.edu.cn -- 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] pme ranks
On 22 Aug 2014, at 12:48, xiexiao...@sjtu.edu.cn wrote: Does anyone know that what the pme ranks mean? See for example [1] in the section Multiple-Program, Multiple-Data PME Parallelization. Best, Carsten 1. Hess, B., Kutzner, C., van der Spoel, D. Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. (2008). xiexiao...@sjtu.edu.cn -- 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] Can we set the number of pure PME nodes when using GPUCPU?
Hi, Because no work will be sent to them. The GPU implementation can accelerate domains from PP ranks on their node, but with an MPMD setup that uses dedicated PME nodes, there will be no PP ranks on nodes that have been set up with only PME ranks. The two offload models (PP work - GPU; PME work - CPU subset) do not work well together, as I said. One can devise various schemes in 4.6/5.0 that could use those GPUs, but they either require * each node does both PME and PP work (thus limiting scaling because of the all-to-all for PME, and perhaps making poor use of locality on multi-socket nodes), or * that all nodes have PP ranks, but only some have PME ranks, and the nodes map their GPUs to PP ranks in a way that is different depending on whether PME ranks are present (which could work well, but relies on the DD load-balancer recognizing and taking advantage of the faster progress of the PP ranks that have better GPU support, and requires that you get very dirty hands laying out PP and PME ranks onto hardware that will later match the requirements of the DD load balancer, and probably that you balance PP-PME load manually) I do not recommend the last approach, because of its complexity. Clearly there are design decisions to improve. Work is underway. Cheers, Mark On Fri, Aug 22, 2014 at 10:11 AM, Theodore Si sjyz...@gmail.com wrote: Hi Mark, Could you tell me why that when we are GPU-CPU nodes as PME-dedicated nodes, the GPU on such nodes will be idle? Theo On 8/11/2014 9:36 PM, Mark Abraham wrote: Hi, What Carsten said, if running on nodes that have GPUs. If running on a mixed setup (some nodes with GPU, some not), then arranging your MPI environment to place PME ranks on CPU-only nodes is probably worthwhile. For example, all your PP ranks first, mapped to GPU nodes, then all your PME ranks, mapped to CPU-only nodes, and then use mdrun -ddorder pp_pme. Mark On Mon, Aug 11, 2014 at 2:45 AM, Theodore Si sjyz...@gmail.com wrote: Hi Mark, This is information of our cluster, could you give us some advice as regards to our cluster so that we can make GMX run faster on our system? Each CPU node has 2 CPUs and each GPU node has 2 CPUs and 2 Nvidia K20M Device Name Device Type Specifications Number CPU NodeIntelH2216JFFKRNodesCPU: 2×Intel Xeon E5-2670(8 Cores, 2.6GHz, 20MB Cache, 8.0GT) Mem: 64GB(8×8GB) ECC Registered DDR3 1600MHz Samsung Memory 332 Fat NodeIntelH2216WPFKRNodesCPU: 2×Intel Xeon E5-2670(8 Cores, 2.6GHz, 20MB Cache, 8.0GT) Mem: 256G(16×16G) ECC Registered DDR3 1600MHz Samsung Memory20 GPU NodeIntelR2208GZ4GC CPU: 2×Intel Xeon E5-2670(8 Cores, 2.6GHz, 20MB Cache, 8.0GT) Mem: 64GB(8×8GB) ECC Registered DDR3 1600MHz Samsung Memory 50 MIC NodeIntelR2208GZ4GC CPU: 2×Intel Xeon E5-2670(8 Cores, 2.6GHz, 20MB Cache, 8.0GT) Mem: 64GB(8×8GB) ECC Registered DDR3 1600MHz Samsung Memory 5 Computing Network SwitchMellanox Infiniband FDR Core Switch 648× FDR Core Switch MSX6536-10R, Mellanox Unified Fabric Manager 1 Mellanox SX1036 40Gb Switch 36× 40Gb Ethernet Switch SX1036, 36× QSFP Interface 1 Management Network Switch Extreme Summit X440-48t-10G 2-layer Switch 48× 1Giga Switch Summit X440-48t-10G, authorized by ExtremeXOS 9 Extreme Summit X650-24X 3-layer Switch 24× 10Giga 3-layer Ethernet Switch Summit X650-24X, authorized by ExtremeXOS1 Parallel StorageDDN Parallel Storage System DDN SFA12K Storage System 1 GPU GPU Accelerator NVIDIA Tesla Kepler K20M70 MIC MIC Intel Xeon Phi 5110P Knights Corner 10 40Gb Ethernet Card MCX314A-BCBTMellanox ConnextX-3 Chip 40Gb Ethernet Card 2× 40Gb Ethernet ports, enough QSFP cables 16 SSD Intel SSD910Intel SSD910 Disk, 400GB, PCIE 80 On 8/10/2014 5:50 AM, Mark Abraham wrote: That's not what I said You can set... -npme behaves the same whether or not GPUs are in use. Using separate ranks for PME caters to trying to minimize the cost of the all-to-all communication of the 3DFFT. That's still relevant when using GPUs, but if separate PME ranks are used, any GPUs on nodes that only have PME ranks are left idle. The most effective approach depends critically on the hardware and simulation setup, and whether you pay money for your hardware. Mark On Sat, Aug 9, 2014 at 2:56 AM, Theodore Si sjyz...@gmail.com wrote: Hi, You mean no matter we use GPU acceleration or not, -npme is just a reference? Why we can't set that to a exact value? On 8/9/2014 5:14 AM, Mark Abraham wrote: You can set the number of PME-only ranks with -npme. Whether it's useful is another matter :-) The CPU-based PME offload and the GPU-based PP offload do not combine very well. Mark On Fri, Aug 8, 2014 at 7:24 AM, Theodore Si sjyz...@gmail.com wrote: Hi, Can we set the number
Re: [gmx-users] Extending simulation problem.
2014-08-21 17:45 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: Well in my *log file nothing about state or *cpi files is mentioned. Sounds like perhaps your combination of circumstances (-append, no old output files provided for appending, maybe not even a checkpoint file provided) is leading to mdrun silently doing the only thing it can do, which is start again from either the -s or -cpi state. Your description of I tried both state.cpt and prev_state.cpt and the beginning of new simulation looks exactly the same doesn't help fully - same as what? The start of the first simulation, or the end of the first simulation? It is exactly the same as the start of the first simulation. Like I said, I did not have appropriate files from previous simulation in my scratch and I rerun it incorrectly I guess. Thank you for your detailed answer :). I think I will manage now to extend this simulation properly. -- 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] Extending simulation problem.
Can you just have a quick look at this? When I run: tpbconv -s npt-md.tpr -extend 95000 -o npt-md.tpr to extend simulation by 95 ns this time I got this message at the end: Extending remaining runtime of by 95000 ps (now 5000 steps) Writing statusfile with starting step 0 and length 5000 steps... time 0.000 and length 10.000 ps So it looks like new status file is written and it says that simulation will start from the very beginning or did I misunderstand something? However when I check state.cpt with gmxdump it looks fine: step = 250 t = 5000.00 as I expect. Thank you, Dawid 2014-08-22 13:15 GMT+01:00 Dawid das add...@googlemail.com: 2014-08-21 17:45 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: Well in my *log file nothing about state or *cpi files is mentioned. Sounds like perhaps your combination of circumstances (-append, no old output files provided for appending, maybe not even a checkpoint file provided) is leading to mdrun silently doing the only thing it can do, which is start again from either the -s or -cpi state. Your description of I tried both state.cpt and prev_state.cpt and the beginning of new simulation looks exactly the same doesn't help fully - same as what? The start of the first simulation, or the end of the first simulation? It is exactly the same as the start of the first simulation. Like I said, I did not have appropriate files from previous simulation in my scratch and I rerun it incorrectly I guess. Thank you for your detailed answer :). I think I will manage now to extend this simulation properly. -- 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] Extending simulation problem.
On 8/22/14, 8:49 AM, Dawid das wrote: Can you just have a quick look at this? When I run: tpbconv -s npt-md.tpr -extend 95000 -o npt-md.tpr to extend simulation by 95 ns this time I got this message at the end: Extending remaining runtime of by 95000 ps (now 5000 steps) Writing statusfile with starting step 0 and length 5000 steps... time 0.000 and length 10.000 ps So it looks like new status file is written and it says that simulation will start from the very beginning or did I misunderstand something? However when I check state.cpt with gmxdump it looks fine: step = 250 t = 5000.00 All of this is expected. Using tpbconv doesn't change the start time of the .tpr file. It says the new .tpr file has a new number of steps and the starting step is determined by the use of a checkpoint file on the mdrun command line. -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] QM/MM simulation: point-charge, pbc and bOPT=yes problems
Dear Gromacs users! I'm trying to interface gromacs (5.0) with orca (2.9.1), although i encountered some problems. I'm testing a tripeptide system which i found here: http://www.picb.ac.cn/~liwenjin/QMMM_simulations/index.html , but i'm using a different .mdp file, with these parameters (i copied the only working configuration): integrator = steep dt = 0.002; ps ! nsteps = 1 nstlist = 10 ns_type = grid rlist = 3.0 rcoulomb= 3.0 coulombtype = cut-off vdwtype = cut-off rvdw= 3.0 pbc = no periodic_molecules = no constraints = none energygrps = QMatoms MMatoms cutoff-scheme = group ; QM/MM calculation stuff QMMM = yes QMMM-grps = QMatoms QMmethod = rhf QMbasis = 3-21G QMMMscheme = normal QMcharge = 0 QMmult = 1 bOPT = no bTS = no SH = no ; ; Energy minimizing stuff ; emtol = 60 ; minimization thresold (kj/mol.nm-1)1 hartree/bohr= 49614.75241 kj/mol.nm-1 1 kj/mol.nm-1=2.01553e-5 hartree/bohr emstep = 0.01 ; minimization step in nm with the .ORCAINFO file of ! LDA cc-(p)VDZ %LJcoefficients peptide.LJ %pointcharges peptide.pc %geom end After i modified the ffnonbonded.itp and atomtypes.atp for the dummy atom, rebuilt the gromacs and the grompp and mdrun commands were executed with the following: grompp -p peptide.top -c peptide.gro -f peptide.mdp -n peptide.ndx -o peptide.tpr mdrun -s peptide.tpr -c peptide.gro -o peptide.trr -e peptide.edr -g peptide.log The first thing is, that the default neighbor searching algorithm - cutoff-scheme=verlet - isn't producing any point charges for ORCA and the job ends with a segmentation fault, although the group cutoff scheme works well. It is not clear to me why this is happening, but i suspect the problem lies in that the qm/mm subrutines are quite old (~2003?), and the verlet scheme introduced much later in gromacs 4.6 (2013). The second problem that i have encountered is with the pbc options: if i'm using pbc=xyz the job terminates with a segmentation fault (core dumped) after orca terminates normally. After i looked for some explanation about coordinate updating on the qmmm.c source file I saw some comments that the update_QMMMrec function not working properly without pbc, even though it works just fine with pbc=no. Little bit confused of that, although the gromacs was tested on the regression package and all the tests passed. The third problem is with the bOPT = yes option. When i pass the optimization to the orca, after the first optimization cycle (before orca terminates normally) the tripeptide's qm region forms an unrealistic geometry. At the input of the second orca run, the qm region scatters, the atoms move apart around 10 angströms from each other and gives the following error message: Error (ORCA_GSTEP): The lambda equations have not converged although, the job continues and at the third orca run gives the following: Calling '/export/home/hegely/Programz/orca_2_9_1_linux_x86-64/orca peptide.inp peptide.out' !!!FATAL ERROR ENCOUNTERED !!! !!!--- !!! !!! I/O OPERATION FAILED!!! ABORTING THE RUN and the job runs onward, giving the same error message over and over until i kill it. In the gromacs .log file no error messages are presented and i don't really have a clue of what's going on. Maybe the point charges destroy the geometry of the peptide? I think i checked all the qm/mm, orca searching results in the gmx-users list, but didn't find the solutions. Sorry if i missed something out, but i would appreciate any help! Bence Hégely -- 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] Interpreting flooding results
Hello Carsten, thanks for replying. Yes, I'm using GMX 4.6.5, so I'm able to see the info in the .xvg file. Best, --- Biological Chemistry and Physics Faculty of Pharmaceutical Sciences at Ribeirão Preto University of São Paulo - Brazil - Mensagem original - De: Carsten Kutzner ckut...@gwdg.de Para: gmx-us...@gromacs.org Enviadas: Sexta-feira, 22 de Agosto de 2014 2:47:40 Assunto: Re: [gmx-users] Interteting flooding results Hi, On 21 Aug 2014, at 23:27, Ricardo O. S. Soares rsoa...@fcfrp.usp.br wrote: Dear users, could anyone give me some general guidelines or links to help me interpret the essential dynamics/flooding output xvg file from a flooding simulation? That depends a bit on which Gromacs Version you are using. If you are using a 4.6 or later version, look in the header of the .xvg file, there should be a short explanation about what is written to each column of the file. What columns are printed depend on what is switched on in your .edi file. Best, Carsten I followed Spiwok's tutorial (http://web.vscht.cz/~spiwokv/mtdec/index.html) and Langer's paper (http://onlinelibrary.wiley.com/doi/10.1002/jcc.20473/full) . Thanks, --- Biological Chemistry and Physics Faculty of Pharmaceutical Sciences at Ribeirão Preto University of São Paulo - Brazil -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Extending simulation problem.
On Aug 22, 2014 2:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/22/14, 8:49 AM, Dawid das wrote: Can you just have a quick look at this? When I run: tpbconv -s npt-md.tpr -extend 95000 -o npt-md.tpr to extend simulation by 95 ns this time I got this message at the end: Extending remaining runtime of by 95000 ps (now 5000 steps) Writing statusfile with starting step 0 and length 5000 steps... time 0.000 and length 10.000 ps So it looks like new status file is written and it says that simulation will start from the very beginning or did I misunderstand something? However when I check state.cpt with gmxdump it looks fine: step = 250 t = 5000.00 All of this is expected. Using tpbconv doesn't change the start time of the .tpr file. It says the new .tpr file has a new number of steps and the starting step is determined by the use of a checkpoint file on the mdrun command line. ... And falling back on the contents of the .tpr to start at the designated start time, if there's no checkpoint provided. Mark -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] QM/MM simulation: point-charge, pbc and bOPT=yes problems
Hi, Unfortunately the QM/MM interface is completely unmaintained, so the fact that it doesn't set fire to your chair is something of a bonus! If you can get the group scheme to do something useful, that's great, but I would suggest you build an older version of GROMACS. In practice, with the impending death of the group scheme, QM/MM support might disappear entirely, unless someone steps up to do the work! Mark On Aug 22, 2014 3:23 PM, Bence Hégely hoemb...@gmail.com wrote: Dear Gromacs users! I'm trying to interface gromacs (5.0) with orca (2.9.1), although i encountered some problems. I'm testing a tripeptide system which i found here: http://www.picb.ac.cn/~liwenjin/QMMM_simulations/index.html , but i'm using a different .mdp file, with these parameters (i copied the only working configuration): integrator = steep dt = 0.002; ps ! nsteps = 1 nstlist = 10 ns_type = grid rlist = 3.0 rcoulomb= 3.0 coulombtype = cut-off vdwtype = cut-off rvdw= 3.0 pbc = no periodic_molecules = no constraints = none energygrps = QMatoms MMatoms cutoff-scheme = group ; QM/MM calculation stuff QMMM = yes QMMM-grps = QMatoms QMmethod = rhf QMbasis = 3-21G QMMMscheme = normal QMcharge = 0 QMmult = 1 bOPT = no bTS = no SH = no ; ; Energy minimizing stuff ; emtol = 60 ; minimization thresold (kj/mol.nm-1)1 hartree/bohr= 49614.75241 kj/mol.nm-1 1 kj/mol.nm-1=2.01553e-5 hartree/bohr emstep = 0.01 ; minimization step in nm with the .ORCAINFO file of ! LDA cc-(p)VDZ %LJcoefficients peptide.LJ %pointcharges peptide.pc %geom end After i modified the ffnonbonded.itp and atomtypes.atp for the dummy atom, rebuilt the gromacs and the grompp and mdrun commands were executed with the following: grompp -p peptide.top -c peptide.gro -f peptide.mdp -n peptide.ndx -o peptide.tpr mdrun -s peptide.tpr -c peptide.gro -o peptide.trr -e peptide.edr -g peptide.log The first thing is, that the default neighbor searching algorithm - cutoff-scheme=verlet - isn't producing any point charges for ORCA and the job ends with a segmentation fault, although the group cutoff scheme works well. It is not clear to me why this is happening, but i suspect the problem lies in that the qm/mm subrutines are quite old (~2003?), and the verlet scheme introduced much later in gromacs 4.6 (2013). The second problem that i have encountered is with the pbc options: if i'm using pbc=xyz the job terminates with a segmentation fault (core dumped) after orca terminates normally. After i looked for some explanation about coordinate updating on the qmmm.c source file I saw some comments that the update_QMMMrec function not working properly without pbc, even though it works just fine with pbc=no. Little bit confused of that, although the gromacs was tested on the regression package and all the tests passed. The third problem is with the bOPT = yes option. When i pass the optimization to the orca, after the first optimization cycle (before orca terminates normally) the tripeptide's qm region forms an unrealistic geometry. At the input of the second orca run, the qm region scatters, the atoms move apart around 10 angströms from each other and gives the following error message: Error (ORCA_GSTEP): The lambda equations have not converged although, the job continues and at the third orca run gives the following: Calling '/export/home/hegely/Programz/orca_2_9_1_linux_x86-64/orca peptide.inp peptide.out' !!!FATAL ERROR ENCOUNTERED !!! !!!--- !!! !!! I/O OPERATION FAILED!!! ABORTING THE RUN and the job runs onward, giving the same error message over and over until i kill it. In the gromacs .log file no error messages are presented and i don't really have a clue of what's going on. Maybe the point charges destroy the geometry of the peptide? I think i checked all the qm/mm, orca searching results in the gmx-users list, but didn't find the solutions. Sorry if i missed something out, but i would appreciate any help! Bence Hégely -- 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
Re: [gmx-users] Numerical Stability of Gromacs Implementation
On Aug 22, 2014 4:49 PM, Johnny Lu johnny.lu...@gmail.com wrote: it has many (relatively) power7 cores and aix 6.1.0.0 with no gpu, and I compiled single precision gromacs 4.6.6 with open mp on it. I tried xlc or mpcc for 30+ times. 6.1 was released 7 years ago, but if you have a functional xlc, then you should be able to build GROMACS. It won't run fast, though. The gcc on it doesn't support openmp, and I compiled another one with openmp, and also gnu cmake. Linker is aix ld, with -lmass, and -lm flags. I am not sure if the mass library helped in compilation of fftw3 library. It doesn't. Somehow, gcc can't find affinity support on aix ld, so I specified that in the job script of llqueue. May be next time I would try the mass simd library(-lmass_simdp7) or vector library (-lmassvp4) (http://www-01.ibm.com/support/docview.wss?uid=swg27005375) Somehow, 24 intel xeon cpu (compiled with intel compiler, and mkl library) seems 4 times faster than 32 power7, when I run gromacs 4.6.6. Not surprising, that Intel hardware has been the target of a lot of optimization. Mark On Thu, Aug 21, 2014 at 7:28 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, Aug 21, 2014 at 7:59 PM, Johnny Lu johnny.lu...@gmail.com wrote: Sorry for asking this. Is it possible for me to get some references about the claims of instability of gromacs simulations, and their debunk? Not really. You can find a paper from some of the Desmond authors that correctly observes some issues in GROMACS 3.x. People occasionally refer to it here as if it is current news. These issues are long fixed, but not worth writing about - journal articles should be about delivering quality science. More commonly, an issue would be handled via private email, though even these are rare. Overall, the biomolecular MD community is quite good at finding problems with their own and each other's algorithms and implementations and getting them fixed constructively. People saying someone said x was bad but gave me no details need to talk to the someone, not just the authors of x ;-) If people start being evasive or secretive about possible problems with their code... be concerned. From the few papers that I read, I guess algorithms of molecular dynamics do not treat all observables equally well. Some old papers say that the velocity in velocity verlet is not symplectic, but rather follows some shadow hamiltonian or generalized equipartition theorem. This is common to all methods with a finite time step - see http://en.wikipedia.org/wiki/Energy_drift. There are certainly a variety of ways of estimating the velocity with common integrators, and they have different quality attributes. You can read about how GROMACS handles this in the manual. Then another one mentioned force splitting can reduce the resonance effect caused by integrator. That said, very few papers talk about this. There are lots of papers that discuss details of multiple time-stepping algorithms that seek to deal with this issue directly. I don't know much about the effect of MD on the observables that I try to look at. It's not an easy topic - generating converged sampling to assess whether an integration scheme correctly samples a complex observable is still a non-trivial matter. That needs to happen before questions of how much algorithmic energy drift is acceptable can be satisfactorily addressed. Until then, claims of my energy conservation is better than yours need to be considered alongside my number of independent converged-ensemble samples is better than yours. And, sorry for replying this late, I have been installing gromacs on aix for a week. Compiling gcc took 3 days of computer time. Seriously, don't bother. I don't think there is any system that would have AIX, with no gcc package available, and which GROMACS 5.0 would run decently on (which would require SIMD support, which currently means x86 or BlueGene/Q). I'd guess your laptop will get equivalent performance. Mark On Thu, Aug 14, 2014 at 2:29 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, Aug 13, 2014 at 1:19 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi again. Some of my friends said that gromacs had lower numerical stability than amber, and occasionally has mysterious error in energy. Show us a result and we'll discuss fixing it ;-) Is that still true? Does the implementation of Integrator cause more resonance effect? Any numerical software can be used poorly. Any numerical software can have bugs. Give them the same input to two implementations of the same algorithm and they should give results that are similar (whatever that means in the problem domain). I am trying to run NVE simulation with the single precision version, and
Re: [gmx-users] Job Submission script for Multiple nodes GPUs
There will be an error if I did mpiexec -np 4 mdrun_mpi -s run.tpr -cpi state.cpt -cpo state.cpt -noappend -gpu_id 01 -nb gpu -ntomp 6 Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 4 PP MPI processes per node, but you provided 2 GPUs. Somehow the system still considers it as a single node. Do you know how to solve it? Good afternoon, I am trying to use multiple nodes to do GPU simulation, each node has two GPUs and 12 CPUs mounted. Is there any submission script for doing that? For single node I used: mpiexec -np 2 mdrun_mpi -s run.tpr -cpi state.cpt -cpo state.cpt -noappend -gpu_id 01 -nb gpu -ntomp 6 For 2 nodes I cannot use the script like mpiexec -np 4 mdrun_mpi -s run.tpr -cpi state.cpt -cpo state.cpt -noappend -gpu_id 0123 -nb gpu -ntomp 6 The -gpu_id string refers to the GPU id?s _per node_, so you should also use -gpu_id 01 on two and more of these nodes. Best, Carsten -- 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] Job Submission script for Multiple nodes GPUs
On 22 Aug 2014, at 18:09, Xingcheng Lin linxingcheng50...@gmail.com wrote: There will be an error if I did mpiexec -np 4 mdrun_mpi -s run.tpr -cpi state.cpt -cpo state.cpt -noappend -gpu_id 01 -nb gpu -ntomp 6 Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 4 PP MPI processes per node, but you provided 2 GPUs. Somehow the system still considers it as a single node. Then your MPI processes are not started correctly across the two nodes. Do you know how to solve it? That depends on the MPI library you are using. Probably you need to specify some kind of a hostfile or machinefile with the names of all nodes. Carsten Good afternoon, I am trying to use multiple nodes to do GPU simulation, each node has two GPUs and 12 CPUs mounted. Is there any submission script for doing that? For single node I used: mpiexec -np 2 mdrun_mpi -s run.tpr -cpi state.cpt -cpo state.cpt -noappend -gpu_id 01 -nb gpu -ntomp 6 For 2 nodes I cannot use the script like mpiexec -np 4 mdrun_mpi -s run.tpr -cpi state.cpt -cpo state.cpt -noappend -gpu_id 0123 -nb gpu -ntomp 6 The -gpu_id string refers to the GPU id?s _per node_, so you should also use -gpu_id 01 on two and more of these nodes. Best, Carsten -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Elastic Network Model
Hello All, I have a quick question regarding Elastic Network model. If the define RUBBER BANDS option is not stated in the .top file, the .itp file (with conditions for if elastic network is on) is same as if it was made with without any elastic network? Please guide. Thanks, sxn -- 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] Elastic Network Model
Hi sxn, Rubber bands... :) So you're talking about a CG topology. If RUBBER_BANDS is not defined, the network is not active. However, they can also be defined in the .mdp file. Furthermore, if you're talking about ElneDyn, then the model is not like regular Martini if you disable the elastic network. Hope it helps, Tsjerk On Aug 22, 2014 7:20 PM, shivangi nangia shivangi.nan...@gmail.com wrote: Hello All, I have a quick question regarding Elastic Network model. If the define RUBBER BANDS option is not stated in the .top file, the .itp file (with conditions for if elastic network is on) is same as if it was made with without any elastic network? Please guide. Thanks, sxn -- 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] (no subject)
Hi Suriyanarayanan, You can check out the WeNMR Gromacs portal. Hope it helps, Tsjerk On Aug 22, 2014 10:29 AM, Balasubramanian Suriyanarayanan bsns...@gmail.com wrote: Dear Users, generally for running a 10 ns simulation is there any online server facility available. This will be helpful for people who do not have a continuous access to the server. regards Suriyanarayanan -- 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] build membrane system from Charmm-Gui
Hi All, I am using POPC/POPG mixed membrane built by Charmm-gui. After remove ions and water from CHARMMGUI pdb and save just the membrane pdb, and use this pdb with pdb2gmx to get top file (I used charmm36), then I would like to know, how to add water and ions back to the system? I read the previous solution was to modify [molecules] in top file (add ions and waters information manually), are there any detailed explanation of how to do that? Thanks very much!! Best, Ning -- 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] build membrane system from Charmm-Gui
On 8/22/14, 4:36 PM, Xiang Ning wrote: Hi All, I am using POPC/POPG mixed membrane built by Charmm-gui. After remove ions and water from CHARMMGUI pdb and save just the membrane pdb, and use this pdb with pdb2gmx to get top file (I used charmm36), then I would like to know, how to add water and ions back to the system? I read the previous solution was to modify [molecules] in top file (add ions and waters information manually), are there any detailed explanation of how to do that? For the coordinates, just paste the water and ion coordinates back into the membrane-only file. For the topology, indeed all you need to do is modify [molecules] in the .top to reflect however many waters and ions there are in the reconstructed system. -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.
