[gmx-users] units for atomic coordinates in traj.xtc? nm?
A very quick question. Can someone confirm that atomic coordinates are stored as in the traj.xtc file in units of nm (as opposed to Angstroms)? I am trying to figure out whether or not in the g_msd program reads in nm or Angstroms. The standard output of the xy graph is nm2 and ps. I can't see that the units are being divided by 10 in the g_msd code so I am guessing the traj.xtc feeds in the units in nm. Just want to be sure... Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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] Instantaneous Square Displacement
Thanks for the advice. I has also found that last source on google and have been thinking how I could apply this. I assume that if I plotted [rt - r0]^2 against time then (for a single molecule) I would get peaks on the graph when the molecules are mobile and dips (where [rt-r0]^2 is close to zero) for the periods where molecules are stuck. This would seem to make sense only for a single molecule (as Mark suggested) as averaged over all molecules, the peaks and troughs would average out and I wouldn't really be illustrating anything. I have made a rough sketch of what the plot should look like and for a few moves of the molecules (using only 15 positions) it seems to make sense. However I don't really find it intuitive given that iSD isn't widely used and for more than a few moves it gets crowded and difficult to interpret. So as I see it, the graph would sample only one molecule over a short time period. Any more thoughts on this? Thanks Jenny Quoting "Justin A. Lemkul" : Mark Abraham wrote: On 8/03/2011 3:01 AM, Jennifer Williams wrote: Hi, I am writing a paper where I describe that gas molecules move inside a pore and then stick for long periods of time in occlusions in the pore wall. A reviewer has mentioned that I could illustrate this effect by using "instantaneous square-displacement". I have already produced MSD vs time plots and used them to obtain the self diffusion coefficient. Can someone shed some light on how I can obtain the instantaneous square displacement in gromacs? I have no idea what "ISD" means, and Google doesn't know either :) Perhaps they want to see the diffusion of a single molecule? Searching for "instantaneous square displacement" turns up very little (3 results), but the last seems to be what you need, as long as this person is correct: http://smartech.gatech.edu/bitstream/handle/1853/13994/bai_xianming_200612_phd.pdf?sequence=1 Section 2.3.3. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 Dr. Jennifer Williams Institute for Materials and Processes School of Engineering University of Edinburgh Sanderson Building The King's Buildings Mayfield Road Edinburgh, EH9 3JL, United Kingdom Phone: ++44 (0)131 650 4 861 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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] using one thermostat for entire system ??
Thanks Mark for the advice. I have just rerun a test simulation with each of my gas species coupled separately to a thermostat and have got similar values for the quantities of interest (diffusion coefficients). However I am not sure that this will satisfy the reviewer without a bit more justification of why I chose to use a single thermostat for my system. I remembered reading some gromacs information on the application of thermostats (on which I based my decision to apply one thermostat for the entire system). I have just managed to locate it on the FAQ page: http://www.gromacs.org/Documentation/Terminology/Thermostats What Not To Do Some hints on practices that generally not a good idea to use: ? Do not use separate thermostats for every component of your system. Some molecular dynamics thermostats only work well in the thermodynamic limit. A group must be of sufficient size to justify its own thermostat. If you use one thermostat for, say, a small molecule, another for protein, and another for water, you are likely introducing errors and artifacts that are hard to predict. In particular, do not couple ions in aqueous solvent in a separate group from that solvent. My system consists of 55 molecules of CO2 38 molecules of N2 3 molecules of O2 One large molecule of MCM-41 (mostly frozen but with mobile surface groups) consisting of 4284 atoms. My take on this was that the gas molecules were in small supply compared to the other part of the system so I should avoid using separate thermostats. Was I mistaken in making this assumption? Is there any feeling for what "sufficient size" as referred to above is? Does anyone know of any papers I could reference in my explanation? Any comments welcome Thanks Jenny Quoting Mark Abraham : On 8/03/2011 2:50 AM, Jennifer Williams wrote: Hi, I simulated the diffusion of small gases (CO2, N2) in a framework structure which was mostly frozen with some mobile surface groups. I applied a temperature thermostat to the entire system (i.e I didn't couple the gas molecules and framework separately). I have now been asked the following by a reviewer: "Please comment on any artefacts that might arise as a result of non-equipartition of energies. For example, what is the calculated temperature of each of the gas species and mobile species?" I have tried to explore the temperature of each species separately but g_energy will only give me the energy of the system as a whole. Are there any other tools within gromacs to look at the temperature of each species in turn from the md runs I already have? Does anyone have a suggestion as to how I can address the reviewer's comment and proove that using one thermostat for the whole system is OK (that is what I am hoping!). Is there anything in particular that I should be looking closely at? g_energy can only report the global temperature as saved in the .edr file, computed during the simulation. The only way of decomposing the temperature is to save velocities to the .trr file with nstvout. (Some colleagues had to do this recently.) Then, judicious use of trjconv to take subsets and matching topology hacking (tpbconv doesn't quite work) mean you can use mdrun -rerun on the subset .trr and matching .tpr to get a group-wise temperature. That can demonstrate whether temperature differentials (ie. heat flows) exist. If you didn't save velocities, you're out of luck. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Dr. Jennifer Williams Institute for Materials and Processes School of Engineering University of Edinburgh Sanderson Building The King's Buildings Mayfield Road Edinburgh, EH9 3JL, United Kingdom Phone: ++44 (0)131 650 4 861 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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] using one thermostat for entire system ??
Hi, I simulated the diffusion of small gases (CO2, N2) in a framework structure which was mostly frozen with some mobile surface groups. I applied a temperature thermostat to the entire system (i.e I didn't couple the gas molecules and framework separately). I have now been asked the following by a reviewer: "Please comment on any artefacts that might arise as a result of non-equipartition of energies. For example, what is the calculated temperature of each of the gas species and mobile species?" I have tried to explore the temperature of each species separately but g_energy will only give me the energy of the system as a whole. Are there any other tools within gromacs to look at the temperature of each species in turn from the md runs I already have? Does anyone have a suggestion as to how I can address the reviewer's comment and proove that using one thermostat for the whole system is OK (that is what I am hoping!). Is there anything in particular that I should be looking closely at? Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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] Instantaneous Square Displacement
Hi, I am writing a paper where I describe that gas molecules move inside a pore and then stick for long periods of time in occlusions in the pore wall. A reviewer has mentioned that I could illustrate this effect by using "instantaneous square-displacement". I have already produced MSD vs time plots and used them to obtain the self diffusion coefficient. Can someone shed some light on how I can obtain the instantaneous square displacement in gromacs? Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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] compiling error in tools
Hello I know this is possibly an issue for the IT support at my Uni but I was wondering if someone could shed some light on what may have gone wrong so at least I can point them in the right direction. As I am getting very small diffusion coefficients when using g_msd, I want to increase the number of decimal points the diffusion coefficient is displayed to. In the file gmx_msd.c within src/tools I changed fprintf(out,"# D[%10s] = %.4f (+/- %.4f) (1e-5 cm^2/s)\n", to fprintf(out,"# D[%10s] = %.8f (+/- %.8f) (1e-5 cm^2/s)\n", then, as I have always done, I just typed in make g_msd to recompile this tool. I get the following error message: src/tools> make g_msd mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/jwillia4/GRO/share/top\" -I/home/jwillia4/GRO/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT g_msd.o -MD -MP -MF .deps/g_msd.Tpo -c -o g_msd.o g_msd.c mv -f .deps/g_msd.Tpo .deps/g_msd.Po /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/home/jwillia4/GRO/lib -lgslcblas -o g_msd g_msd.o libgmxana_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la -lgsl -lnsl -lfftw3f -lm mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o g_msd g_msd.o -L/home/jwillia4/GRO/lib ./.libs/libgmxana_mpi.a /home/jwillia4/GRO/gromacs-4.0.7/src/mdlib/.libs/libmd_mpi.a ../mdlib/.libs/libmd_mpi.a /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a ../gmxlib/.libs/libgmx_mpi.a /home/jwillia4/GRO/lib/libgslcblas.so /home/jwillia4/GRO/lib/libgsl.so -lnsl /home/jwillia4/GRO/lib/libfftw3f.a -lm -Wl,--rpath -Wl,/home/jwillia4/GRO/lib -Wl,--rpath -Wl,/home/jwillia4/GRO/lib /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(main.o): In function `init_par': main.c:(.text+0xc0): undefined reference to `ompi_mpi_comm_world' main.c:(.text+0xc8): undefined reference to `ompi_mpi_comm_world' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(main.o): In function `init_multisystem': main.c:(.text+0xb99): undefined reference to `ompi_mpi_comm_world' main.c:(.text+0xbd9): undefined reference to `ompi_mpi_comm_world' main.c:(.text+0xbee): undefined reference to `ompi_mpi_comm_world' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):network.c:(.text+0x15): more undefined references to `ompi_mpi_comm_world' follow /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumi_sim': network.c:(.text+0x96): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x9b): undefined reference to `ompi_mpi_int' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumf_sim': network.c:(.text+0x4e6): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x4eb): undefined reference to `ompi_mpi_float' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumd_sim': network.c:(.text+0x9a6): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x9ab): undefined reference to `ompi_mpi_double' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumi': network.c:(.text+0xe8f): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0xe94): undefined reference to `ompi_mpi_int' network.c:(.text+0xec0): undefined reference to `ompi_mpi_int' network.c:(.text+0xed7): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0xedc): undefined reference to `ompi_mpi_int' network.c:(.text+0x12fe): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1303): undefined reference to `ompi_mpi_int' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumf': network.c:(.text+0x134e): undefined reference to `ompi_mpi_float' network.c:(.text+0x1354): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1380): undefined reference to `ompi_mpi_float' network.c:(.text+0x1397): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x139c): undefined reference to `ompi_mpi_float' network.c:(.text+0x183e): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1843): undefined reference to `ompi_mpi_float' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumd': network.c:(.text+0x1890): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1895): undefined reference to `ompi_mpi_double' network.c:(.text+0x18c2): undefined reference to `ompi_mpi_double' network.c:(.text+0x18d7): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x18dc): undefined reference to `ompi_mpi_double' network.c:(.text+0x1d86): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1d8b): undefined reference to `ompi_mpi_double' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_m
[gmx-users] energy group exlusions for frozen structures-use of maxwarn -1?
Hello. I am using a porous structure (MOF). I am interested in how guest molecules inside the porous structure interact with each other and the pores of the structure. As my structure represents a rigid crystalline framework it is usually kept rigid/frozen and only non bonded parameters (LJ and electrostatics) are taken into account for this structure. (I think) I read somewhere on the forum the energy group exclusions should be applied for frozen atoms (also if I don?t do this I get some v. large energies). So I use the following in my .mdp file ; Selection of energy groups energygrps = MOF ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = MOF MOF However on running grompp I get the following warning: WARNING 1 [file MCM_TDI.top, line 32874]: Can not exclude the lattice Coulomb energy between energy groups Why is this? My frozen structure has partial charges but is overall charge neutral. To get around this I have to use maxwarn -1. I am a bit wary of using maxwarn. Can someone advise whether it is sensible to use maxwarn in this case? Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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] genconf to insert small molecules triclinic unit cell
Hi Justin, The .pdb I sent with my last e-mail was a result of trying to add 500 molecules. The max of 168 were added and then genconf couldn't add anymore despite the large vacant space. Trying to add more molecules to this .pdb won't work. This is what makes me think the space was somehow inaccessible. If I carry out an mdrun on this structure, the NO molecules distribute themselves into this empty space. If I take the structure file following MD I can add an extra 24 molecules with genbox. The worry is not for these small NO molecules where I can use MD to create more space. I am also trying to insert larger organic molecules and if parts of the unit cell are seen as inaccessible I won't be able to get the molecules in there in the first place. Jenny Quoting "Justin A. Lemkul" : Jennifer Williams wrote: Hi Justin, Thanks for the response (again!). I would be happy if genbox inserted molecules randomly (within the box defined by my .pdf file) but the output doesn't look random but subject to some strange (symmetry?)constraints which don't allow random insertions into some areas of my unit cell. The molecules will crowd into one space leaving another portion of the cell completely empty. The inserted molecules assume the shape of a box whilst the rest of my structure is a triclinic cell. One pic is probably worth a thousand words. I've attached a .pdb of the final structure. I'd appreciate if you could tell me if this is normal output for genbox, I see nothing wrong with it. Looks like genbox started adding molecules on one "side" of your box, and continued adding until it reached 100, then stopped. Looks like you simply have more than enough space to add more of your NO molecules, that's all. The molecules are all within the unit cell, so I see no issue. If you want a more homogeneous distribution of NO, you may have to come up with a different method. -Justin Thanks very much Jenny Quoting "Justin A. Lemkul" : Jennifer Williams wrote: Hi, I have a strange problem when I try to insert small molecules into my cell using genconf. Here the cell is a crystalline metal-organic framework with lots of space for the molecules inside. The edges of the metal organic framework defined the pbcs. When I view the final structure, the inserted molecules appear to have a different symmetry to that of the MOF/cell. They notieably avoid some empty regions inside the box and are inserted outside regions of my triclinic cell. The inserted molecules don?t occupy a triclinic shape at all. I have used this feature before on a similar triclinic cell and it worked perfectly. I can?t tell what I am doing wrong this time. I outline the steps I take below. 1. I am trying to insert a number of molecules of NO into a triclinic crystal cell. The pdb file of the crystal cell has the following cell parameters. CRYST1 25.885 25.8856.806 90.00 90.00 120.00 P 1 1 This is the pdb file of the small molecule I am trying to insert: CRYST1 25.885 25.885 27.2232 90.00 90.00 120.00 P 1 1 HETATM1 NNO NOO 1 1.150 0.000 0.000 1.00 0.00 N HETATM2 ONO NOO 1 0.000 0.000 0.000 1.00 0.00 O CONECT12 END I use the following commands: To centre the cell: editconf -c -f MOF.pdb -o MOF_centered.pdb To make a 1x1x4 box ( I need to increase the length in z) so that I can use sensible cut-offs later on genconf -nbox 1 1 4 -f MOF_centered.pdb -o MOF_4c.pdb To add the NO molecules: genbox ?cp MOF_4c.pdb -ci NOO.pdb -nmol 100 -o inserted_NO.pdb Any ideas appreciated as I have been going around in circles. When using genbox -ci, there is no guarantee of any type of symmetry. It inserts molecules randomly, wherever it finds space. I don't think you're doing anything wrong, I think you're just encountering a limitation of genbox. -Justin I am using gromacs 4.0.7 Thanks Jenny -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee D
[gmx-users] genconf to insert small molecules triclinic unit cell
Hi, I have a strange problem when I try to insert small molecules into my cell using genconf. Here the cell is a crystalline metal-organic framework with lots of space for the molecules inside. The edges of the metal organic framework defined the pbcs. When I view the final structure, the inserted molecules appear to have a different symmetry to that of the MOF/cell. They notieably avoid some empty regions inside the box and are inserted outside regions of my triclinic cell. The inserted molecules don?t occupy a triclinic shape at all. I have used this feature before on a similar triclinic cell and it worked perfectly. I can?t tell what I am doing wrong this time. I outline the steps I take below. 1. I am trying to insert a number of molecules of NO into a triclinic crystal cell. The pdb file of the crystal cell has the following cell parameters. CRYST1 25.885 25.8856.806 90.00 90.00 120.00 P 1 1 This is the pdb file of the small molecule I am trying to insert: CRYST1 25.885 25.885 27.2232 90.00 90.00 120.00 P 1 1 HETATM1 NNO NOO 1 1.150 0.000 0.000 1.00 0.00 N HETATM2 ONO NOO 1 0.000 0.000 0.000 1.00 0.00 O CONECT12 END I use the following commands: To centre the cell: editconf -c -f MOF.pdb -o MOF_centered.pdb To make a 1x1x4 box ( I need to increase the length in z) so that I can use sensible cut-offs later on genconf -nbox 1 1 4 -f MOF_centered.pdb -o MOF_4c.pdb To add the NO molecules: genbox ?cp MOF_4c.pdb -ci NOO.pdb -nmol 100 -o inserted_NO.pdb Any ideas appreciated as I have been going around in circles. I am using gromacs 4.0.7 Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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] Polar Hydrogen missing using PRODRG
Hi, So, I did as suggested. Ran PRODRG the first time using the JME Editor and took the pdb file from this. Then I added the ADDHYD OAE underneath (actually it doesn't matter which O (OAD or OAE) is protonated as long as it is only one of them). The first bit of output looked encouraging... PRODRG> PDB mode detected. PRODRG> Molecule complexity index: 2.00. PRODRG> Added hydrogen on atom OAE . PRODRG> 18 hydrogen(s) added. PRODRG> Using charge groups. PRODRG> Net charge on molecule: 0.000 PRODRG> 20 partial charges 0 ambiguous PRODRG> Cannot assign type to atom ' OAE'. ERRDRG> Error in GROMOS atom names/types. PRODRG> Program terminated unsuccessfully, sorry! So it understood that I wanted a hydrogen and the net charge is at last 0(usually -1 without that hydrogen) but then it crashes! I don't understand why it can't assign a type to OAE. IS it because a hydrogen is now attached so the hybridisation has changed from sp2 to sp3? Do I need to change the identity of OAE before putting a hydrogen on? If so to what? Thanks Jenny REMARK REMARK REMARK This file was generated by PRODRG version 071121.0636 REMARK PRODRG written/copyrighted by Daan van Aalten REMARK and Alexander Schuettelkopf REMARK REMARK Questions/comments to d...@davapc1.bioch.dundee.ac.uk REMARK REMARK When using this software in a publication, cite: REMARK A. W. Schuettelkopf and D. M. F. van Aalten (2004). REMARK PRODRG - a tool for high-throughput crystallography REMARK of protein-ligand complexes. REMARK Acta Crystallogr. D60, 1355--1363. REMARK REMARK HETATM1 CAA DRG 1 2.360 1.610 1.840 1.00 20.00 C HETATM2 CAN DRG 1 3.580 2.340 1.260 1.00 20.00 C HETATM3 CAB DRG 1 3.330 2.650 -0.210 1.00 20.00 C HETATM4 CAJ DRG 1 4.820 1.450 1.460 1.00 20.00 C HETATM5 CAL DRG 1 6.160 2.130 1.140 1.00 20.00 C HETATM6 CAG DRG 1 6.870 1.740 -0.010 1.00 20.00 C HETATM7 CAI DRG 1 8.100 2.360 -0.300 1.00 20.00 C HETATM8 CAF DRG 1 6.640 3.140 2.010 1.00 20.00 C HETATM9 CAH DRG 1 7.870 3.760 1.720 1.00 20.00 C HETATM 10 CAM DRG 1 8.600 3.370 0.570 1.00 20.00 C HETATM 11 CAO DRG 1 9.930 4.110 0.310 1.00 20.00 C HETATM 12 CAC DRG 1 10.120 4.580 -1.140 1.00 20.00 C HETATM 13 CAK DRG 1 11.150 3.250 0.700 1.00 20.00 C HETATM 14 OAE DRG 1 12.100 3.870 1.240 1.00 20.00 O HETATM 15 OAD DRG 1 11.130 2.020 0.480 1.00 20.00 O CONECT12 CONECT2134 CONECT32 CONECT425 CONECT5468 CONECT657 CONECT76 10 CONECT859 CONECT98 10 CONECT 1079 11 CONECT 11 10 12 13 CONECT 12 11 CONECT 13 11 14 15 CONECT 14 13 CONECT 15 13 END ADDHYD OAE Quoting "Justin A. Lemkul" : You need to run PRODRG twice. The first time, do not use ADDHYD. Make note of the atom names that PRODRG assigns. Then run PRODRG a second time, using ADDHYD with the atom name that PRODRG uses for the O atom you want protonated. -Justin Jennifer Williams wrote: Hi Justin, Thanks for your answer. The ADDHYD in the FAQ sounds like exactly what I need however I can't get this command to work. I draw in my molecule using the JME editor and get this .pdb file in the PRODRG window. CC(C)Cc1ccc(C(C)C(=O)O)cc1 JME 2002.05 Thu Oct 14 10:48:38 BST 2010 15 15V2000 0.0.0. C 1.21242.10000. C 7.27464.20000. C 8.48700.70000. O 9.69952.80000. O 3.63732.10000. C 4.84970.0. C 4.84972.80000. C 6.06220.70000. C 2.42490.0. C 8.48702.10000. C 3.63730.70000. C 6.06222.10000. C 1.21240.70000. C 7.27462.80000. C 1 14 1 0 2 14 1 0 3 15 1 0 4 11 2 0 5 11 1 0 6 8 1 0 6 12 2 0 7 9 2 0 7 12 1 0 8 13 2 0 9 13 1 0 10 12 1 0 10 14 1 0 11 15 1 0 13 15 1 0 M END If I then try adding ADDHYD O to the window and clicking "run PRODRG" I get the following: ERRDRG> Atom 'O' referenced in instruction was not found. PRODRG> Program terminated unsuccessfully, sorry! I've then tried renaming O to OM as there are 2 Os in my structure and I only want one protonated. However, no other name is recognized so I get this message: ERRDRG> Currently o
Re: [gmx-users] Polar Hydrogen missing using PRODRG
Hi Justin, Thanks for your answer. The ADDHYD in the FAQ sounds like exactly what I need however I can't get this command to work. I draw in my molecule using the JME editor and get this .pdb file in the PRODRG window. CC(C)Cc1ccc(C(C)C(=O)O)cc1 JME 2002.05 Thu Oct 14 10:48:38 BST 2010 15 15V2000 0.0.0. C 1.21242.10000. C 7.27464.20000. C 8.48700.70000. O 9.69952.80000. O 3.63732.10000. C 4.84970.0. C 4.84972.80000. C 6.06220.70000. C 2.42490.0. C 8.48702.10000. C 3.63730.70000. C 6.06222.10000. C 1.21240.70000. C 7.27462.80000. C 1 14 1 0 2 14 1 0 3 15 1 0 4 11 2 0 5 11 1 0 6 8 1 0 6 12 2 0 7 9 2 0 7 12 1 0 8 13 2 0 9 13 1 0 10 12 1 0 10 14 1 0 11 15 1 0 13 15 1 0 M END If I then try adding ADDHYD O to the window and clicking "run PRODRG" I get the following: ERRDRG> Atom 'O' referenced in instruction was not found. PRODRG> Program terminated unsuccessfully, sorry! I've then tried renaming O to OM as there are 2 Os in my structure and I only want one protonated. However, no other name is recognized so I get this message: ERRDRG> Currently only N, C, O, S, P, Cl, Br, F, I are supported. PRODRG> Program terminated unsuccessfully, sorry! Next I tried using the PDB generated by PRODRG and repasting it with the ADDHYD command into the PRODRG window. Now the pdb looks like this: REMARK REMARK REMARK This file was generated by PRODRG version 071121.0636 REMARK PRODRG written/copyrighted by Daan van Aalten REMARK and Alexander Schuettelkopf REMARK REMARK Questions/comments to d...@davapc1.bioch.dundee.ac.uk REMARK REMARK When using this software in a publication, cite: REMARK A. W. Schuettelkopf and D. M. F. van Aalten (2004). REMARK PRODRG - a tool for high-throughput crystallography REMARK of protein-ligand complexes. REMARK Acta Crystallogr. D60, 1355--1363. REMARK REMARK HETATM1 CAA DRG 1 2.360 1.610 1.840 1.00 20.00 C HETATM2 CAN DRG 1 3.580 2.340 1.260 1.00 20.00 C HETATM3 CAB DRG 1 3.330 2.650 -0.210 1.00 20.00 C HETATM4 CAJ DRG 1 4.820 1.450 1.460 1.00 20.00 C HETATM5 CAL DRG 1 6.160 2.130 1.140 1.00 20.00 C HETATM6 CAG DRG 1 6.870 1.740 -0.010 1.00 20.00 C HETATM7 CAI DRG 1 8.100 2.360 -0.300 1.00 20.00 C HETATM8 CAF DRG 1 6.640 3.140 2.010 1.00 20.00 C HETATM9 CAH DRG 1 7.870 3.760 1.720 1.00 20.00 C HETATM 10 CAM DRG 1 8.600 3.370 0.570 1.00 20.00 C HETATM 11 CAO DRG 1 9.930 4.110 0.310 1.00 20.00 C HETATM 12 CAC DRG 1 10.120 4.580 -1.140 1.00 20.00 C HETATM 13 CAK DRG 1 11.150 3.250 0.700 1.00 20.00 C HETATM 14 OAE DRG 1 12.100 3.870 1.240 1.00 20.00 O HETATM 15 OAD DRG 1 11.130 2.020 0.480 1.00 20.00 O CONECT12 CONECT2134 CONECT32 CONECT425 CONECT5468 CONECT657 CONECT76 10 CONECT859 CONECT98 10 CONECT 1079 11 CONECT 11 10 12 13 CONECT 12 11 CONECT 13 11 14 15 CONECT 14 13 CONECT 15 13 END I've tried changing the HETATM to OM and using ADDHYD OM and then played around with various other things like renaming the atom symbol at the end of the line and even the OAD, DRG but I always get the following: ERRDRG> Atom 'OM' referenced in instruction was not found. PRODRG> Program terminated unsuccessfully, sorry! I am using the PRODRG beta server available online at http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta Will I fare any better if I use the source code or is there something obvious I am doing wrong? Does the ADDHYD have to be added in any particular location of the pdb file? I have tried a few random positions including at the very top, very bottom and just beneath the O to be protonated. Nothing worked. Any ideas much appreciated, Jenny Quoting "Justin A. Lemkul" : Jennifer Williams wrote: Hi, I am trying to get a .itp file for a simple molecule (Ibuprofen). This contains a COOH group. THe problem is that PRODRG removes the polar hydrogen of the COOH from the .pdb file and generates a .itp file without it. I am not concerned about the other aromatic hydrogens but I really need
[gmx-users] Polar Hydrogen missing using PRODRG
Hi, I am trying to get a .itp file for a simple molecule (Ibuprofen). This contains a COOH group. THe problem is that PRODRG removes the polar hydrogen of the COOH from the .pdb file and generates a .itp file without it. I am not concerned about the other aromatic hydrogens but I really need the polar hydrogen modelled explicitly. Is there a fix for this within PRODRG? I know I can use pdb2gmx to add hydrogens but the residue names of the pdb file are not recognized by the existing forcefields so I usually bypass using pdb2gmx. Thanks Jenny Dr. Jennifer Williams Institute for Materials and Processes School of Engineering University of Edinburgh Sanderson Building The King's Buildings Mayfield Road Edinburgh, EH9 3JL, United Kingdom Phone: ++44 (0)131 650 4 861 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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] Convert LJ 9-6 to LJ 12-6?
Hi I want to check some of my gromacs results using another computer program which is set up to read in LJ 12-6 parameters only. I have a set of 9-6 LJ parameters. Can gromacs interconvert LJ-9-6 to 12-6? If not can anyone point me in the right direction to a paper, bit of code etc. Changing the source code of the other program to read in LJ 9-6 is something I'd rather avoid if there is another solution. Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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] pbc in one direction only for analysis?
Dear gromacs users I have surface groups anchored on a cylindrical pore wall (similar to a carbon nanotube). The pore runs along the z direction. I am trying to determine to what extent my surface groups are clustered together and was thinking of using g_mindist and/or g_rdf for this analysis. I usually work with periodic boundary conditions in all 3 directions for MD runs. The problem I have is that I want to use periodic boundaries only in the z direction and not the x and y for the anaysis. I.e I dont want the surface groups in my pore to see other surface groups in neighbouring cells in the x or y direction. From what I can see, the options with g_rdf is either to have pbc in all 3 directions or not at all. Does anyone know a way around this? I am analyzing one pdb file and not a trajectory. I am using gromacs 4.0.7 Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Can I make make_ndx interactive?
Hi, Is there some way of making the make_ndx file interactive so that I can include it in a script? I would usually type in "a C_O and O_C" to select my atoms I've tried altering the example on the webpage for making commands interactive: make_ndx -flags
[gmx-users] Re: Can I make make_ndx interactive?
I realised "flags" is not part of the command. !! Sorry for the silly question. It's the end of a long day and I'm tired! Quoting Jennifer Williams : Hi, Is there some way of making the make_ndx file interactive so that I can include it in a script? I would usually type in "a C_O and O_C" to select my atoms I've tried altering the example on the webpage for making commands interactive: make_ndx -flags < -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] no non bonded parameters from PRODRG
Hi, I am trying to create .top files for some complex organic molecules using the PRODRG server and the gromos 96 forcefield. PRODRG gives me bonded parameters (stretching, angle bending, torsions) etc but no lennard jones parameters (sigma, epsilon) or charges. Where can I get the non bonded terms from? Does it make sense to extract these values from the OPLS forcefield or elsewhere when I am using gromas 96 forcefield to get the bonded parameters. I am wary of cobbelling forcefield parameters together from different sources, Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] High quality movies, bmp frames and videomach=poor quality
Hi, I am using tachyon to get high quality still pictures by generating a .dat file, changing the render numbers and then typing this command in the window "N:/myhome/VMD1.8.7/tachyon_WIN32.exe" -aasamples 12 plot01.dat -format -o plot01.tga This gives great images but now I am stuck on generating movies as I don?t seem to have much choice when using the movie-maker and am clueless at scripting. I need a movie file in .mpg or .avi for submission to a journal (and not bigger than 10MB). Whenever I choose tachyon as the renderer within the movie maker I get frames generated in .dat which I can?t do anything with and when I use tachyon internal the files are automatically written in .bmp. I can?t seem to get my frames in targa or any format other than .bmp. Is there a script command which could give me high quality snapshots in .tga? If I continue with my frames in .bmp and generate a movie in videomach the image quality is very poor (I do this via preview movie and select the highest quality (fast 400x400). TO avoid this I have been using convert in unix to stick frames together but this won't give me a mpg or avi file! Can anyone give me some advice or a script line similar to the one above which would work on a whole trajectory rather than a single frame?. Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] reference for gromos 87 within PRODRG
Hi, I have generated some topology files using the gromos87 forcefield within the PRODRG server. Does anyone have a reference for this force-field? I can't seem to find it, Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] compilation problems orte error
Sorry for the delay in replying back. I start the job using the following script file: #$ -S /bin/bash #$ -l h_rt=47:59:00 #$ -j y #$ -pe mpich2 8 #$ -cwd cd /home/jwillia4/GRO/gromacs-4.0.7/JJW_003/PH_TORUN /home/jwillia4/GRO/bin/mpirun -np 8 /home/jwillia4/GRO/bin/mdrun_mpi -v -s md.tpr The strange thing is that sometimes it works and the job runs to completion and sometimes it crashes immediately with the orte error so I know that it is not the input files causing the problems. It seems entirely random. Has it to do with the -pe mpich2 8 line? I was previously using Open MPI installed on the cluster for common use but now have downloaded everything into my home directory. The script has been adapted from the time when I didn't have my own OpenMPI in my home directory. Perhaps it needs further alteration but I don't know what. How would I do about checking whether MPI is running? If you spot anything suspicious in the above commands please let me know. Thanks Jenny Quoting Chandan Choudhury : As Justin said give the command line options for mdrun and also check that your mpi environment is running. Better to run a parallel job and check its output. Chadnan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Feb 8, 2010 at 8:02 PM, Justin A. Lemkul wrote: Jennifer Williams wrote: Dear All, I am having problems compiling gromacs 4.0.7 in parallel. I am following the Quick and Dirty Installation instructions on the gromacs webpage. I downloaded the the versions of fftw, OpenMPI and gromacs-4.0.7 following these instructions. Everything seems to compile OK and I get all the serial executables including mdrun written to my bin directory and they seem to run fine. However when I try to run mdrun_mpi on 6 nodes I get the following: [vlxbig16:08666] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08667] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08700] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08670] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08681] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08659] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 -- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_rml_base_select failed --> Returned value -13 instead of ORTE_SUCCESS Does anyone have any idea what is causing this? Computer support at my University is not sure. How are you launching mdrun_mpi (command line)? -Justin Thanks -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php Dr. Jennifer Williams Institute for Materials and Processes School of Engineering University of Edinburgh Sanderson Building The King's Buildings Mayfield Road Edinburgh, EH9 3JL, United Kingdom Phone: ++44 (0)131 650 4 861 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] compilation problems orte error
Dear All, I am having problems compiling gromacs 4.0.7 in parallel. I am following the Quick and Dirty Installation instructions on the gromacs webpage. I downloaded the the versions of fftw, OpenMPI and gromacs-4.0.7 following these instructions. Everything seems to compile OK and I get all the serial executables including mdrun written to my bin directory and they seem to run fine. However when I try to run mdrun_mpi on 6 nodes I get the following: [vlxbig16:08666] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08667] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08700] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08670] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08681] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 [vlxbig16:08659] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 -- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_rml_base_select failed --> Returned value -13 instead of ORTE_SUCCESS Does anyone have any idea what is causing this? Computer support at my University is not sure. Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] g_sdf and visualizing using gOpenMol
Hi, I have a mesoporous silica with attached organic surface groups (alkyl chains). I am trying to quantify to what extent these surface groups interact with the mesoporous silica surface they are attached to (as opposed to projecting straight into the pore space). I thought about using the g_sdf tool (on one surface group at a time initially) but am not completely sure what I am doing is correct so I am hoping someone can guide me. My index file looks like this [MCM] 1 [MCM] 2 [MCM] 3 [SI] 4 5 6 7 8 9 10 11 12 13 Where groups 1, 2 and 3 are carbons of the alkyl chain. SI atoms are taken to represent the surface of the mesoporous silica. I run g_sdf in gromacs and get a refmol.gro file (which looks very different to my structure) and a gom_plt.dat file. I've installed gOpenMol but I am having trouble loading the gom_plt.dat file. It is necessary to load coordinates in first so I load in refmol.gro. As soon as I try to load the .dat file (using plot> contour>import) the gui window closes and I get the following Will apply a physical translation (x,y,z): 12.236523 18.866343 9.419045 Will apply a MT translation (x,y,z): 0.07 0.04 0.02 Minimum value 0.00 maximum value 134.129913 Signal was caught => : Success Signal code is: 11, errno I am not sure whether this is because I have unreasonable data in my .dat file (or because my refmol.gro file looks strange) or because I haven't got the hang of using gOpenMol. I don't have any idea what the contour plot should like. Could someone e-mail me a working gom_plt.dat file so I can at least check that I can correctly load it and see what a plot looks like? Any further advice is appreciated, Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc
Hi Justin Thanks for the suggestions. However, I don't really want to stop the molecule moving into the next image-I start off with an alkyl chain where a large portion of the structure overlaps the pbc. i.e C1-C2-C3 \\ C4-C5-C6 where || is the unit cell boundary. To see the whole alkyl chain I use the graphics/representations/periodic tab in VMD. The problem is that VMD will not allow me to draw a bond between C3 and C4 meaning I get odd looking movies. VMD prefers to join the C3 to the C4 in the same unit cell rather than the C4 sitting right next to it on the other side of the pbc. This means long bonds stretching the length of my unit cell and missing bonds between atoms sitting next to each other! I have spent a while trying to solve this and have posted to the VMD forum (as it is actually a problem with VMD and not gromacs). If I could somehow do the same thing to the traj.xtc as I did to confgro.out using genconf -nbox 2 2 2 that would solve my visualisation problem. Do you know of a way to do this? Even a round-about way? I suppose if I dumped each frame in the trajectory as a pdb, used genbox on them to get a 2x2x2 box and then somehow stuck them together into an .xtc this might work (but any suggestions which are less messy are greatly appreciated!) Jenny Quoting "Justin A. Lemkul" : Jennifer Williams wrote: Hello, I am trying to find a way around a visualisation problem I am having in VMD. Some of my molecules go over periodic boundary conditions meaning that bonds sometimes appear missing when looking at movies (I am trying to fix this using wrap, unwrap and join in VMD but as yet no luck). I was wondering if there is a way in gromacs to multiply the number of unit cells shown in a trajectory. i.e instead of a 1x1x1 I want the new unit cell to be 2x2x2. This would mean the section of the structure I want to zoom in doesn't go over the pbc. For the confout.gro file I have done this using genconf -nbox 2 2 2 -f confout.gro -o confbig.out and this enables me to at least see a static image where all bonds are present. but in order to view a movie, I need to carry out something similar on the traj.xtc file. I have seen that with trjconv there is the option -box Size for new cubic box but my unit cell is not cubic, it is a parallelepiped. The cell dimensions are : 4.64210 3.77847 1.89596 0.0 0.0 -2.18150 0.0 0.0 0.0 I tried using this anyway with the following command: trjconv -box 9.28414 8.72598 3.79192 -f traj.xtc -o trajbig.xtc but the resulting .xtc file wouldn't load into VMD so I assume that the .xtc file and the .gro file didn't match. Correcting periodicity should alleviate some of the problems. Using trjconv -pbc mol (or -pbc nojump) is typically the best first step. -Justin Any ideas?, Thanks Jenny -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php Dr. Jennifer Williams Institute for Materials and Processes School of Engineering University of Edinburgh Sanderson Building The King's Buildings Mayfield Road Edinburgh, EH9 3JL, United Kingdom Phone: ++44 (0)131 650 4 861 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc
Hello, I am trying to find a way around a visualisation problem I am having in VMD. Some of my molecules go over periodic boundary conditions meaning that bonds sometimes appear missing when looking at movies (I am trying to fix this using wrap, unwrap and join in VMD but as yet no luck). I was wondering if there is a way in gromacs to multiply the number of unit cells shown in a trajectory. i.e instead of a 1x1x1 I want the new unit cell to be 2x2x2. This would mean the section of the structure I want to zoom in doesn't go over the pbc. For the confout.gro file I have done this using genconf -nbox 2 2 2 -f confout.gro -o confbig.out and this enables me to at least see a static image where all bonds are present. but in order to view a movie, I need to carry out something similar on the traj.xtc file. I have seen that with trjconv there is the option -box Size for new cubic box but my unit cell is not cubic, it is a parallelepiped. The cell dimensions are : 4.64210 3.77847 1.89596 0.0 0.0 -2.18150 0.0 0.0 0.0 I tried using this anyway with the following command: trjconv -box 9.28414 8.72598 3.79192 -f traj.xtc -o trajbig.xtc but the resulting .xtc file wouldn't load into VMD so I assume that the .xtc file and the .gro file didn't match. Any ideas?, Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] functional form of PRODRG dihedrals
Hello, I have a general question re the PRODRG server used to create topologies for gromacs. Using PRODRG for a simple alkane I get: [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 4 3 2 1 1 0.05.9 3 0.05.9 3 ; dih CAG CAE CAC The dihedrals created are given the function fu = 1 so I assume that they are not Ryckaert-Bellemans functions (where fu=3). What is the functional form of the dihedral given by PRODRG? Does it correspond to equation 4.6.1 on page 62 of the gromacs manual (v. 4.0)? If so which numbers in the above dihedral correspond to the symbols in equation 4.6.1? Thanks Jenny Dr. Jennifer Williams Institute for Materials and Processes School of Engineering University of Edinburgh Sanderson Building The King's Buildings Mayfield Road Edinburgh, EH9 3JL, United Kingdom Phone: ++44 (0)131 650 4 861 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Charge group moving too much
Hello, One of my simulations just crashed after 660,000 steps with the following message: Step 660560: The charge group starting at atom 4100 moved than the distance allowed by the domain decomposition (1.50) in direction X distance out of cell 2.356293 Old coordinates:1.7520.4470.751 New coordinates:3.5931.5320.674 Old cell boundaries in direction X:0.0002.116 New cell boundaries in direction X:0.0002.122 --- Program mdrun, VERSION 4.0.5 Source code file: domdec.c, line: 3651 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated --- "Why Weren't You at My Funeral ?" (G. Groenhof) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 8 I am modelling flexible alkyl chains which are anchored to a frozen silica wall. This particular atom (4100) is at the edge of the periodic boundary condition so I am guessing that what happens is that while the anchored side stays where it is, the other free end wanders into the next cell and this perhaps triggers the error message? If this is indeed the problem, is there some way to stop the program stopping with an error message when this happens? I did do an energy minimisation before starting and my structure looks OK. It seems strange that it would crash only after 66 steps. Also what is meant by the following? I am using NVT so my simulation cell should not change. Old cell boundaries in direction X:0.0002.116 New cell boundaries in direction X:0.0002.122 My cell is about 4.3 x 4.3 x 7.5 nm I am using gromacs-4.0.5 Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Freezing a molecule
Hello, One quick questions... I have a structure for which I now want to freeze a portion. I already have a .top file where the entire structure is flexible (bond angles, stretches and torions defined). When freezing, do I need to delete all those bond stretches, angles and torsions associated with the frozen part from my .top file? (I am not using constraints on the frozen portion as I have seen this can cause problems). Will the bonding parameters all be set to zero when the these atoms are frozen or will their contribution be calculated if I leave these terms in. Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells
serint4 = 0 userreal1= 0 userreal2= 0 userreal3= 0 userreal4= 0 grpopts: nrdf:5392 ref_t: 300 tau_t: 0.1 anneal: No ann_npoints: 0 acc:0 0 0 nfreeze: Y Y Y N N N energygrp_flags[ 0]: 0 efield-x: n = 0 efield-xt: n = 0 efield-y: n = 0 efield-yt: n = 0 efield-z: n = 0 efield-zt: n = 0 bQMMM= FALSE QMconstraints= 0 QMMMscheme = 0 scalefactor = 1 qm_opts: ngQM = 0 Initializing Domain Decomposition on 8 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition NOTE: Periodic molecules: can not easily determine the required minimum bonded cut-off, using half the non-bonded cut-off Minimum cell size due to bonded interactions: 0.750 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.376 nm Estimated maximum distance required for P-LINCS: 0.376 nm Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 0.938 nm The maximum allowed number of cells is: X 4 Y 4 Z 8 Domain decomposition grid 2 x 1 x 4, separate PME nodes 0 Domain decomposition nodeid 0, coordinates 0 0 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Will do PME sum in reciprocal space. PLEASE READ AND CITE THE FOLLOWING REFERENCE U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 --- Thank You --- Using a Gaussian width (1/beta) of 0.480244 nm for Ewald Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.2 System total charge: 0.000 Generated table with 2000 data points for Ewald. Tabscale = 500 points/nm Generated table with 2000 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 2000 data points for LJ12Shift. Tabscale = 500 points/nm Generated table with 2000 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 2000 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 2000 data points for 1-4 LJ12. Tabscale = 500 points/nm Configuring nonbonded kernels... Testing x86_64 SSE support... present. Initializing Parallel LINear Constraint Solver PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 --- Thank You --- The number of constraints is 800 There are inter charge-group constraints, will communicate selected coordinates each lincs iteration Linking all bonded interactions to atoms There are 3236 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: X 1 Z 1 The initial domain decomposition cell size is: X 2.01 nm Z 1.90 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.500 nm two-body bonded interactions (-rdd) 1.500 nm multi-body bonded interactions (-rdd) 1.500 nm atoms separated by up to 5 constraints (-rcon) 1.896 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Z 1 The minimum size for domain decomposition cells is 1.500 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.75 Z 0.79 The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.500 nm two-body bonded interactions (-rdd) 1.500 nm multi-body bonded interactions (-rdd) 1.500 nm atoms separated by up to 5 constraints (-rcon) 1.500 nm Making 2D domain decomposition grid 2 x 1 x 4, home cell index 0 0 0 There are: 5244 Atoms There are: 476 VSites Charge group distribution at step 0: 583 565 583 565 666 684 666 684 Grid: 9 x 6 x 6 cells Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) Not all bonded interactions have been properly assigned to the domain decomposition cells Dr. Jennifer Williams Institute for Materials and Processes School of Engineering University of Edinburgh Sanderson Building The King's Buildings Mayfield Road Edinburgh, EH9 3JL, United Kingdom Phone: ++44 (0)131 650 4 861 -- The University of Edinburgh is a charitable body, registered in Scotland,
Re: [gmx-users] how to stop duplicate atoms from being deleted
Hi Justin, Thanks for the new suggestion. However, wouldn't this again involve the sorting of my .pdb file? I have modified the specbond.dat 3 MSI SI4 MOO 2 0.16 MCM MCM MSI SI4 MOH OH2 0.16 MCM MCM MOH OH2 MHH 1 0.101 MCM MCM BUT the specbond.dat is called after the duplicate atoms are deleted: Now there are 4 atoms. Deleted 4280 duplicates. Opening library file /home/jwillia4/gromacs-4.0.5/code/share/gromacs/top/specbond.dat 3 out of 3 lines of specbond.dat converted succesfully So at present my pdb file is shortened down to 4 atoms before specdat even gets a chance to work on it. The only solution I can see to this is to rename each and every atom in my .pdb file with a different residue number and name. This then means that I would need a huge specbond.dat where the bonds were defined for each of these residues-this would essentially mean defining thousands of bonds as I wouldn't be able to define the bonds by atom type but by their individual reside number. Is this correct or am I missing something? What I really would like is to stop the program deleting these duplicate atoms-then I could use pdb2gmx to generate the entire topology file. Do you know a way of doing this (and here I am really hoping that I don't have to mess with the source code :) )? Thanks -I am learning a lot from your advice Jenny Quoting "Justin A. Lemkul" : Justin A. Lemkul wrote: I can see how this rapidly becomes difficult :) I don't believe that pdb2gmx can handle such "multi-directional" bonding, since the residues that are connected are not necessarily numerically sequential. I should amend this statement (typing quicker than the brain can keep up!) - It is not that pdb2gmx cannot handle multi-directional bonding, it is moreso that I don't think it cannot be done using the +/- convention of the .rtp files. Using specbond.dat, as I suggested before, should be a viable alternative. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php Dr. Jennifer Williams Institute for Materials and Processes School of Engineering University of Edinburgh Sanderson Building The King's Buildings Mayfield Road Edinburgh, EH9 3JL, United Kingdom Phone: ++44 (0)131 650 4 861 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] how to stop duplicate atoms from being deleted
which oxygens belong to which monomer. The only way I can see past this is a more elaborate naming system which would introduce yet more combinations. So I?m throwing this out as a last resort before I give up. Has anyone had any success using this method for a similar system? Quartz? Sorry for my rambling Jenny Quoting "Justin A. Lemkul" : Jennifer Williams wrote: Hi Justin, Thanks for the reply. I am in fact studying one huge molecule. All of my atoms are bonded together in one large structure (kind of like a zeolite) so I have necessarily defined them as a single residue. I would argue that you have a polymer, which can certainly be handled by pdb2gmx. See below. There is no way I can split this molecule into smaller subunits and thus define a number of residues-it wouldn't make sense to do so. If you have a lot of repetition, I would think it would be quite easy to split it apart. Yes in my .rtp file I have only defined each atom type once. To define each and every atom in my one residue would mean defining 4284 atoms! If you have a repeating structure, you have a polymer, so you can just decompose a repeat unit into a single .rtp entry. That's the entire purpose of pdb2gmx, we certainly wouldn't want to create an .rtp entry for every single possible protein either! For more information, see here: http://www.gromacs.org/Documentation/How-tos/Polymers I am having real trouble in creating topology files for my structure. At the moment, the only way I can do this is by using a tool in DL_POLY to create a field file and then manually change it to a .top file. This is really fiddely and I have a number of similar structures to do this for. I was hoping that I could do a similar step in Gromacs and get a .top file straight away-even if it means a bit more work setting it up. Is there any hope or is pdb2gmx simply not designed to work for this sort of system? You can certainly use pdb2gmx, it is intended to be versatile so it can be used with any repeating structure of monomers, homogenous (like a repeating polymer) or heterogenous (like a protein). See the link above. -Justin Thanks Jenny Quoting "Justin A. Lemkul" : Quoting Jennifer Williams : Hello I am studying a mesoporous silica for which there is no topology in gromacs-to try to automate the process of generating a topology file (x2top doesn?t work), I am using pdb2gmx (or rather trying to). I have parameters for my silica structure and have added a new section for my molecule to the .rtp file, .atp file, atommass.dat, atom_nom.dbl, nb.itp and bon.itp files. The problem is that when I use my .pdb file to generate a topology, pdb2gmx checks for duplicates and removes almost all of my atoms. It leaves only one of each type. I should have a few hundred of each atom type?here is the output from pdb2gmx? Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 4284 atoms chain #res #atoms 1 ' ' 1 4284 All occupancies are one All ok up to here?and then?. Processing chain 1 (4284 atoms, 1 residues) There are 552 donors and 2580 acceptors There are 1603 hydrogen bonds Checking for duplicate atoms Now there are 4 atoms. Deleted 4280 duplicates. Can anyone explain why this is happening? ?none of my atoms have the same coordinates. Is there a file that I have forgotten to alter? Is there is fix to turn off the checking of duplicate atoms? I don?t want any of my atoms to be deleted! You have all of your atoms defined within one residue. I'm assuming your .rtp entry contains the definition of a single repeat unit, so each monomer should be a separate residue. The coordinates don't matter, it's because within each residue, you have the same atom names, so pdb2gmx removes them when it finds them. Below I paste an extract of my pdb file? I'm assuming you'll have to probably reconstruct this file to re-organize the atoms to define continuous residues. It appears they are grouped by atom name, which is probably not what you want. -Justin CRYST1 46.421 43.630 75.838 90.00 90.00 120.00 P 1 1 ATOM 1 SI MCM 1 -21.090 -1.951 -29.596 1.00 0.00 SI ATOM 2 SI MCM 1 -21.090 -1.951 -10.636 1.00 0.00 SI ??.. ATOM 1153 OMCM 1 20.602 -18.404 -20.904 1.00 0.00 O ATOM 1154 OMCM 1 20.602 -18.404 -1.945 1.00 0.00 O ? ATOM 3181 OH MCM 1 -6.620 -18.769 -32.169 1.00 0.00 ATOM 3182 OH MCM 1 -6.620 -18.769 -13.210 1.00 0.00 . ATOM 3733 HMCM 1 -6.674 -18.381 -33.035 1.00 0.00 H ATOM 3734 HMCM 1 -6.616 -18.600 -14.144 1.00 0.00 H Any advice appreciated, Thanks in advance -- The University of Edinburgh is a char
Re: [gmx-users] how to stop duplicate atoms from being deleted
Hi Justin, Thanks for the reply. I am in fact studying one huge molecule. All of my atoms are bonded together in one large structure (kind of like a zeolite) so I have necessarily defined them as a single residue. There is no way I can split this molecule into smaller subunits and thus define a number of residues-it wouldn't make sense to do so. Yes in my .rtp file I have only defined each atom type once. To define each and every atom in my one residue would mean defining 4284 atoms! I am having real trouble in creating topology files for my structure. At the moment, the only way I can do this is by using a tool in DL_POLY to create a field file and then manually change it to a .top file. This is really fiddely and I have a number of similar structures to do this for. I was hoping that I could do a similar step in Gromacs and get a .top file straight away-even if it means a bit more work setting it up. Is there any hope or is pdb2gmx simply not designed to work for this sort of system? Thanks Jenny Quoting "Justin A. Lemkul" : Quoting Jennifer Williams : Hello I am studying a mesoporous silica for which there is no topology in gromacs-to try to automate the process of generating a topology file (x2top doesn?t work), I am using pdb2gmx (or rather trying to). I have parameters for my silica structure and have added a new section for my molecule to the .rtp file, .atp file, atommass.dat, atom_nom.dbl, nb.itp and bon.itp files. The problem is that when I use my .pdb file to generate a topology, pdb2gmx checks for duplicates and removes almost all of my atoms. It leaves only one of each type. I should have a few hundred of each atom type?here is the output from pdb2gmx? Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 4284 atoms chain #res #atoms 1 ' ' 1 4284 All occupancies are one All ok up to here?and then?. Processing chain 1 (4284 atoms, 1 residues) There are 552 donors and 2580 acceptors There are 1603 hydrogen bonds Checking for duplicate atoms Now there are 4 atoms. Deleted 4280 duplicates. Can anyone explain why this is happening? ?none of my atoms have the same coordinates. Is there a file that I have forgotten to alter? Is there is fix to turn off the checking of duplicate atoms? I don?t want any of my atoms to be deleted! You have all of your atoms defined within one residue. I'm assuming your .rtp entry contains the definition of a single repeat unit, so each monomer should be a separate residue. The coordinates don't matter, it's because within each residue, you have the same atom names, so pdb2gmx removes them when it finds them. Below I paste an extract of my pdb file? I'm assuming you'll have to probably reconstruct this file to re-organize the atoms to define continuous residues. It appears they are grouped by atom name, which is probably not what you want. -Justin CRYST1 46.421 43.630 75.838 90.00 90.00 120.00 P 1 1 ATOM 1 SI MCM 1 -21.090 -1.951 -29.596 1.00 0.00 SI ATOM 2 SI MCM 1 -21.090 -1.951 -10.636 1.00 0.00 SI ??.. ATOM 1153 OMCM 1 20.602 -18.404 -20.904 1.00 0.00 O ATOM 1154 OMCM 1 20.602 -18.404 -1.945 1.00 0.00 O ? ATOM 3181 OH MCM 1 -6.620 -18.769 -32.169 1.00 0.00 ATOM 3182 OH MCM 1 -6.620 -18.769 -13.210 1.00 0.00 . ATOM 3733 HMCM 1 -6.674 -18.381 -33.035 1.00 0.00 H ATOM 3734 HMCM 1 -6.616 -18.600 -14.144 1.00 0.00 H Any advice appreciated, Thanks in advance -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@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/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/mailing_lists/users.php
[gmx-users] how to stop duplicate atoms from being deleted
Hello I am studying a mesoporous silica for which there is no topology in gromacs-to try to automate the process of generating a topology file (x2top doesn?t work), I am using pdb2gmx (or rather trying to). I have parameters for my silica structure and have added a new section for my molecule to the .rtp file, .atp file, atommass.dat, atom_nom.dbl, nb.itp and bon.itp files. The problem is that when I use my .pdb file to generate a topology, pdb2gmx checks for duplicates and removes almost all of my atoms. It leaves only one of each type. I should have a few hundred of each atom type?here is the output from pdb2gmx? Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 4284 atoms chain #res #atoms 1 ' ' 1 4284 All occupancies are one All ok up to here?and then?. Processing chain 1 (4284 atoms, 1 residues) There are 552 donors and 2580 acceptors There are 1603 hydrogen bonds Checking for duplicate atoms Now there are 4 atoms. Deleted 4280 duplicates. Can anyone explain why this is happening? ?none of my atoms have the same coordinates. Is there a file that I have forgotten to alter? Is there is fix to turn off the checking of duplicate atoms? I don?t want any of my atoms to be deleted! Below I paste an extract of my pdb file? CRYST1 46.421 43.630 75.838 90.00 90.00 120.00 P 1 1 ATOM 1 SI MCM 1 -21.090 -1.951 -29.596 1.00 0.00 SI ATOM 2 SI MCM 1 -21.090 -1.951 -10.636 1.00 0.00 SI ??.. ATOM 1153 OMCM 1 20.602 -18.404 -20.904 1.00 0.00 O ATOM 1154 OMCM 1 20.602 -18.404 -1.945 1.00 0.00 O ? ATOM 3181 OH MCM 1 -6.620 -18.769 -32.169 1.00 0.00 ATOM 3182 OH MCM 1 -6.620 -18.769 -13.210 1.00 0.00 . ATOM 3733 HMCM 1 -6.674 -18.381 -33.035 1.00 0.00 H ATOM 3734 HMCM 1 -6.616 -18.600 -14.144 1.00 0.00 H Any advice appreciated, Thanks in advance -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] msd not linear and c.o.m removal
Hi, I am running simulations of gaseous molecules (CH4, C2H6, CO2, N2) in a silica pore (4nm in diameter), cell dimensions, 46 x 44 x 37. This in an infinite pore in the z direction. I am interested in looking at diffusion but I am a bit concerned about the shape of my MSD curves, for a 5ns run, they start off fairly linear and then at around 2.5ns the slope stops being linear and levels out - in some cases the gradient goes to zero. So I am getting a curve rather than a straight line. This is the same whether or not I use the ?type z option in my command. At the moment I take the fit the curve between 0.5 - 2.5ns and ignore the second curvy half of the graph but I'd like to know why this is happening-Is it because the statistics become poorer for longer runs or is there something fundamentaly wrong with my system?. Does anyone know why this is happening? Another thing I am confused about is whether or not to remove the centre of mass when one is interested in obtaining the diffusion coefficient. I have seen on the gromacs forum that linear centre of mass removal is OK but a colleague has advised me not to remove it when studying diffusion. What about when applying an acceleration to obtain transport diffusion coefficients? Is c.o.m removal then needed or not? Currently, I am not using any centre of mass removal in my mdrun. Then I calculate the Ds to be g_msd ?mol -type z -f traj.xtc -s md.tpr -o msd_z.xvg D[ CO2] 140.5914 (+/- 75.9583) 1e-5 cm^2/s However when I include the ?rmcomm command when I run g_msd I get a very different Ds. g_msd -rmcomm -type z -mol -f traj.xtc -s md.tpr -o msd_z.xvg D[ CO2] 0.0118 (+/- 0.0364) 1e-5 cm^2/s It is difficult to say which value is correct as we don't have experimental data for comparison. Has anyone got any advice on this? I have pasted my typical input files below Much appreciated, C2H6.itp [ atomtypes ] ; typemasschargeptype c6c12 CH315.034 0.00 A0.35121.16236218 [ moleculetype ] ; name nrexcl ET 2 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 CH3 1 ET CH3 10.000 15.03452 2 CH3 1 ET CH3 10.000 15.03452 [ constraints ] ; ai aj funct c0 c1 1 2 1 0.2353 [ exclusions ] 1 2 2 1 .mdp ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = -I../top ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 500 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= none ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = yes ; nblist cut-off rlist= 1.5 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.5 ; Relative dielectric constant for the medium and the reaction field epsilon-r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Shift ; cut-off lengths rvdw-switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables betw
[gmx-users] large scaling required to acheive optimal mesh load
Hello user, I am simulating a unit cell with dimensions 70x70x38 nm using PME. I started out with a cut-off of rvdw = rcoloumb = rlist=0.9 and a Spacing for the PME/PPPM FFT grid= 0.12, optimize fft = yes I get the following output when I compile the .tpr file: Using a fourier grid of 60x60x33, spacing 0.117 0.117 0.117 Estimate for the relative computational load of the PME mesh part: 0.97 NOTE 1 [file SMO_CO2.top, line 2159]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing I did a number of test-runs increasing the cut-offs and the grid spacing by a factor of themselves. However I had to nearly double the cut-off and grid spacing in order to get the PME mesh load below 50. From the forum notes on the topic I got the impression that only a small scaling factor was needed. My question is, are the values which I have achieved reasonable? Cut-off: 1.665 and grid spacing 0.222 This is the output using these values Checking consistency between energy and charge groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 32x32x18, spacing 0.219 0.219 0.215 Estimate for the relative computational load of the PME mesh part: 0.38 This run will generate roughly 63 Mb of data writing run input file... Does changing these values have any effect on the results of the mdrun or only on the speed? Thanks in advance, Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] potential energy NaN and strange dependence on cut-offs
Hi users, I am running a very simple simulation of methane inside a pore (v.much like a carbon nanotube but in my case the tube is supposed to represent silica.) I keep this tube frozen. I start with an energy minimisation-however this runs to completion almost instantly and I keep get NaN for my potential energy: Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax < 10. Potential Energy =nan Maximum force = 6.5738518e+01 on atom 2133 Norm of force = 1.5461593e+00 Otherwise the trajectory looks OK (methane moving around inside the cylinder). If I go on to use the conf.gro file for an mdrun, it runs to completion and generates what looks like a reasonable trajectory, however the output again contains NaN i.e: Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy nan0.0e+00nan3.36749e+01nan Conserved En.Temperature Pressure (bar) nan3.00010e+02nan and calculating the Diffusion coefficient gives: D[ CH4] 613.6682 (+/- 97.0563) 1e-5 cm^2/s If I do the same calculation but reduce the cut-offs to 0.9. I get Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy nan0.0e+00nan3.36750e+01nan Conserved En.Temperature Pressure (bar) nan3.00011e+02nan D[ CH4] 237.8712 (+/- 53.5975) 1e-5 cm^2/s And for a cut-off of 1.3nm I get Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energ y nan0.0e+00nan3.36737e+01na n Conserved En.Temperature Pressure (bar) nan2.9e+02nan D[ CH4] 19.7953 (+/- 154.0168) 1e-5 cm^2/s For this system, the cut-off shouldn?t need to be larger than 0.8 (I have plotted graphs of calculated V vs r) so it is worrying that the diffusion coefficient is showing such dependence on the cut-offs when they should all give the same result. Can anyone offer any insight into this? I?ve tried changing the timestep making it both larger and smaller and many other things. I?ve pasted the relevant parts of my files below: I?m using gromacs 4.0.5 ?at the moment running in serial. Thanks for any advice, Top file [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.01.0 ; ; [ atomtypes ] ; typemasschargeptype c6c12 OSM15.99940.00 A 0.2708 1.538176 ; ; Include forcefield parameters #include "CH4.itp" ; ; [ moleculetype ] ; Namenrexcl MCM 3 [ atoms ] ; nr typeresnr residue atomcgnrcharge mass 1 OSM 1 MCM OSM 1 0 15.9994 2 OSM 1 MCM OSM 2 0 15.9994 ..etc 2127OSM 1 MCM OSM 21270 15.9994 2128OSM 1 MCM OSM 21280 15.9994 [ system ] ; Name CH4 in MCM [ molecules ] ; Compound#mols MCM1 CH410 CH4.itp file [ atomtypes ] ; type masschargeptype c6c12 CH416.043 0.00 A0.37321.24650457 ; [ moleculetype ] ; name nrexcl CH42 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 CH4 1 CH4 CH4 10.00 16.043 .mdp file ; ; File 'mdout.mdp' was generated ; By user: jwillia4 (353773) ; On host: vlxhead2 ; At date: Fri Jun 26 15:47:37 2009 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = -I../top ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit= 0 dt = 0.0001 nsteps = 10 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= emstep = 0.001 ; Max number of iterations in relax_shells niter= ; Step size (ps^2) for minimization of flexibl
RE: [gmx-users] very strange domain composition statistics
Quoting Jennifer Williams : Hi, Thanks for your input. Sorry I should have mentioned that I am using the latest version of gromacs (4.0.5). This morning I noticed that the strange domain decomp statistics are only produced when my simulations run on certain nodes. Below I have pasted the domain decomp statistics for the SAME .tpr file run on 2 different nodes (each time using 6 nodes)- the first looks ok to me while the second produces crazy numbers. I have opened a call to computer support at my Uni to ask if there is some difference between the nodes and for now I specify that my simulations should run on certain nodes which I have checked are ok. I don't know if this is something to do with the way I compiled gromacs or the architecture. I did a standard installation and it seemed to run smoothly-no error messages. I have attached my config.log. If you have any ideas please let me know, Thanks D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 1967.2 av. #atoms communicated per step for LINCS: 2 x 20.4 Average load imbalance: 30.3 % Part of the total run time spent waiting due to load imbalance: 5.8 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 % NOTE: 5.8 % performance was lost due to load imbalance in the domain decomposition. R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp. 6 11 852.216 341.9 3.0 Comm. coord. 6101 594.411 238.5 2.1 Neighbor search6 11 2271.294 911.2 7.9 Force 6101 5560.129 2230.519.3 Wait + Comm. F 6101 1216.171 487.9 4.2 PME mesh 610115071.432 6046.152.2 Write traj.6 10012.5771.0 0.0 Update 6101 264.545 106.1 0.9 Constraints6101 923.418 370.4 3.2 Comm. energies 6101 942.036 377.9 3.3 Rest 61167.866 468.5 4.0 --- Total 6 28866.09611580.0 100.0 --- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 1930.000 1930.000100.0 32:10 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 51.737 6.922 44.767 0.536 Finished mdrun on node 0 Fri Jul 31 13:05:01 2009 D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 1969.0 av. #atoms communicated per step for LINCS: 2 x 15.7 Average load imbalance: 500.0 % Part of the total run time spent waiting due to load imbalance: 5822746112.0 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 % NOTE: 5822746112.0 % performance was lost due to load imbalance in the domain decomposition. R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Write traj.6 1001 18443320128.89043061.8 100.0 Update 6101 314.1750.0 0.0 Rest 69223372036.85521534.950.0 --- Total 618443397799.33643062.0 100.0 --- NOTE: 306 % of the run time was spent communicating energies, you might want to use the -nosum option of mdrun Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 7177.000 7177.000100.0 1h59:37 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 13.907 1.861 12.038 1.994 Finished mdrun on node 0 Thu Jul 30 01:47:05 2009 Quoting Berk Hess : Date: Fri, 31 Jul 2009 07:49:49 +0200 From: sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] very strange domain composition statistics Mark Abraham wrote: Jennifer Williams wrote: Hi , I am having some problems when running in parallel. Although my jobs run to completion I am getting some worrying domain decomposition statistics in particular the average load imbalance and the performance loss due to load imbalance see below: Please report your GROMACS version number. If it&
[gmx-users] very strange domain composition statistics
Hi , I am having some problems when running in parallel. Although my jobs run to completion I am getting some worrying domain decomposition statistics in particular the average load imbalance and the performance loss due to load imbalance see below: D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 1974.8 av. #atoms communicated per step for LINCS: 2 x 15.2 Average load imbalance: 500.0 % Part of the total run time spent waiting due to load imbalance: 4246403072.0 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 % NOTE: 4246403072.0 % performance was lost due to load imbalance in the domain decomposition. R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Write traj.6 1001 18443320139.16442130.9 100.0 Update 6101 18442922984.49142130.0 100.0 Rest 69223372036.85521069.450.0 --- Total 618446422611.66942138.0 100.0 --- NOTE: 305 % of the run time was spent communicating energies, you might want to use the -nosum option of mdrun Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 7023.000 7023.000100.0 1h57:03 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 14.214 1.902 12.302 1.951 Finished mdrun on node 0 Wed Jul 29 23:47:18 2009 Below is my .mdp file: I am using the PME but not having much of a feel for how to set the options under Spacing for the PME/PPPM FFT grid, I left these as the default values. Could this be where the trouble lies? My cut-off cannot be larger than 0.9 as my unit cell is only 18.2A in one direction. How do I choose values for PME/PPPM? Ie what kind of values to use for nx, ny and nz ? I read that they should be divisible by npme to get the best performance. Is npme the pme_order in the .mdp file? If not where do I set this parameter? Much appreciated, Jenny ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = -I../top ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 100 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= emstep = ; Max number of iterations in relax_shells niter= ; Step size (ps^2) for minimization of flexible constraints fcstep = ; Frequency of steepest descents steps when doing CG nstcgsteep = nbfgscorr= ; TEST PARTICLE INSERTION OPTIONS rtpi = ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = yes ; nblist cut-off rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Relative dielectric constant for the medium and the reaction field epsilon_r
Re: [gmx-users] Huge acceleration needed to reproduce results!
Hi Chris, Thanks for the input-its good to get another person's perspective. Let me explain a bit more about my system... MCM stands for MCM-41, a mesoporous silica which consits of 1071 atoms so even though it is only 1 molecule, it is the more massive group. I am purposely accelerating the methane to try and calculate their diffusion thourgh the pore of the MCM. As I understand it, the acceleration I specify should be applied to each and every molecule of CH4. I.e if I specify an acceleration of 0.1 nm ps-2, each of my 340 molecules should experience an acceleration of 0.1. I.e the acceleration is not in any way divided up between the total number of accelerated molecules? Jenny Quoting chris.ne...@utoronto.ca: Title indicates you think that you have CH4 in MCM: [ system ] ; Name CH4 in MCM Actual system is MCM in CH4: [ molecules ] ; Compound#mols MCM1 CH4340 .mdp accelerates the CH4: acc-grps = CH4 Now I'm not sure if this is the source of any problem, equal and opposite being true, but you are certainly trying to accelerate the more massive group and it seems like a strange thing to do. Could this be it? Chris. -- original message -- Quoting Jennifer Williams : Hi, Yes I realised that gromacs works in ps. I converted my force in kj mol-1 A-1 to acceleration in nm/ps2. I also took into account that the msd.xvg is plotted in nm and ps-2 and the calculated gradient printed at the top of the msd.xvg file is in cm2/s. One strange thing that I do get is the message ?There were 228 inconsistent shifts. Check your topology? when I carry out the g_msd with the ?mol option but not when I don?t use -mol. Why is this? I also came across a forum post (http://www.mail-archive.com/gmx-users@gromacs.org/msg5.html) that said ?If the distance between two atoms is close to half the box, the force may arbitrarily change sign. This is an ill-defined situation for which there is no obvious solution.? Could this somehow be affecting my simulations? Below are the relevant parts of my .mdp file and other files. If you see something suspicious please let me know because I?m stuck, Thanks ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 100 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = yes ; nblist cut-off rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Relative dielectric constant for the medium and the reaction field epsilon_r= epsilon_rf = ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = nose-hoover ; Groups to couple separate
Re: [gmx-users] Huge acceleration needed to reproduce results!
Hi, Yes I realised that gromacs works in ps. I converted my force in kj mol-1 A-1 to acceleration in nm/ps2. I also took into account that the msd.xvg is plotted in nm and ps-2 and the calculated gradient printed at the top of the msd.xvg file is in cm2/s. One strange thing that I do get is the message ?There were 228 inconsistent shifts. Check your topology? when I carry out the g_msd with the ?mol option but not when I don?t use -mol. Why is this? I also came across a forum post (http://www.mail-archive.com/gmx-users@gromacs.org/msg5.html) that said ?If the distance between two atoms is close to half the box, the force may arbitrarily change sign. This is an ill-defined situation for which there is no obvious solution.? Could this somehow be affecting my simulations? Below are the relevant parts of my .mdp file and other files. If you see something suspicious please let me know because I?m stuck, Thanks ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 100 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = yes ; nblist cut-off rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Relative dielectric constant for the medium and the reaction field epsilon_r= epsilon_rf = ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = nose-hoover ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 150 ; Pressure coupling Pcoupl = No Pcoupltype = ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= compressibility = ref-p= ; Scaling of reference coordinates, No, All or COM refcoord_scaling = no ; Random seed for Andersen thermostat andersen_seed= ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 150 gen_seed = 173529 ; OPTIONS FOR BONDS constraints = none ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration continuation = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR= no ; Relative tolerance of shake shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it sho
[gmx-users] Huge acceleration needed to reproduce results!
Hello users, I am trying to reproduce a calculation that I carried out in DL_POLY. It is to calculate the transport diffusion coefficient for CH4 in a frozen mesoporous silica. In DL_POLY I used an external force of 0.1 kJ mol-1 A-1. (0.1 KJ per mole per angstrom). This equates to 10 dl_poly internal units which I add in this way at each timestep; Fsum = Fsum + Fex In Gromacs, I want to apply the same force as I used in DL_POLY so I calculated the required acceleration using F=ma. Where I took the mass to be the mass of one molecule of methane (16 a.m.u). The final value for acceleration that I came up with (which corresponds to a force of 0.1kj mol-1 A-1 on each molecule) was 0.0625 nm ps-2. The first hiccup was when I used this value, the MSD was negative (though linear in the negative region of the graph). I assumed that this had something to do with the orientation of the unit cell and tried applying 0.0 0.0 -0.0625. The plot then looked much better. The problem is when I calculate the Mean displacement of the CH4 molecules. (I do this using a slightly altered version of the g_msd code). The Mean displacement from gromacs is very different to that which I calculate using DL_POLY, Gromacs gives 95.0, dl_poly 21347.0. The MSD however (where I don?t add an acceleration are similar) so the problem lies with the force I am adding. To test that it wasn?t some bug in my code to calculate the Mean displacement, I also looked at how the acceleration/force altered the MSD in DL_POLY and gromacs. In DL_POLY, adding an external force of 0.1kj mol-1 A-1 would change the MSD of methane by 3 orders of magnitude compared to a run with no force added. My equivalent acceleration of -0.0625 in gromacs, in comparison, barely changes the MSD from that of a run with no acceleration added. In fact it takes an acceleration of -200 in the z direction to cause such a difference in the Ds coefficients between runs with and without acceleration. Does anyone have any idea what is going on here? An acceleration of 200 ps nm-2 surely is not reasonable is it?. It seems very large compared to the example in the manual of 0.1. This would then imply that my back of the envelope calculation for relating force and acceleration is wrong. Am I missing something? I?m quite sure that the force I am adding in DL_POLY is equivalent to 0.1 kJ mol-1 A-1 so why are my methane molecules moving so much less in gromacs in response to the equivalent acceleration? Also I noticed that although in the .mdp file I specify: ; Non-equilibrium MD stuff acc-grps = CH4 accelerate = 0.0 0.0 -200.00 In the md.log file I get the following output acc:0 0-154.549 0 0 45.4514 Can someone clarify what this means? Any advice/comments appreciated -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] questions on acceleration
Hello, I have 3 short questions regarding adding an acceleration. 1. I want to apply a force in the z direction to some of my molecules to mimic a chemical potential gradient. I read an old gmx_users post where someone wanted to add an external force to their molecules and the advice given was to add a piece of code after the function efield in the code in src/mdlib/sim_util.c . That is, to make a function similar to efield which would do Fsum = Fsum + Fext Is there any reason for doing this rather than using the accelerate option in the .mdp file? 2. If I do use the accelerate option in the .mdp file, I need to convert the acceleration applied into a force. Just to check?. I assume that if I use F=ma, where F and a are the force and acceleration applied to a molecule, then m should be the mass of that molecule? I.e for a CO2 molecule, m will be 44 a.m.u? 3. If I use the accelerate option under NEMD, does it still make sense to remove the C.O.M? Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Changing gmx_msd.c
Hi gmx_users, I am trying to use NEMD to get transport diffusion coefficients. I am adding an acceleration to my atoms in the z direction and then I need to calculate this quantity: 1/t < ? [r(t) ? r(0)] > My plan was to alter the code that calculates the MSD (gmx_msd.c located in src/tools). This calculates; 1/t < 1/N. ? [r(t) ? r(0)]^2 > I presumed that all I needed to do was locate and remove the squared function and the division by the number of molecules (1/N). I would also change the factor for the conversion of nm^2/ps to 10e-5 cm^2/s since I would now be doing nm/ps to 10e-5 cm/s. However my problem is that I have never worked with C++ so changing the code involved some guess-work. For the removal of the square I did; r2 += rv[m]*rv[m]; > r2 += rv[m]; (line 252) r2 += r*r; > r2 += r;(line 270) to remove the division by the number of molecules (1/N), I removed line g/=nx; (line 279) I realise that these changes are only valid for the first case CASE (static_real_calc_norm), which I presumed was for the basic calculation invoked by this command; g_msd ?f traj.xtc ?s md.tpr i.e. I don?t plan on using ?pbc ?mol etc so I didn?t change the code for these cases. (I also realise that unless I change the code, the calculated error wont be valid-but I was going to worry about that later!) However, the changes I made do not change the output from that of the original MSD code. I am using the correct, changed executable and not an old one (i.e I copied the compiled executable to gromacs/bin). So it looks like I am not changing the correct part of the code, or perhaps the command line g_msd ?f traj.xtc ?s md.tpr is not changing the case I altered? Has anyone else changed the code for this purpose or would anyone be able to give me some pointers on what I need to alter in the code. Today is the first time I have ever looked at any C++ code (though I know some fortran) so please be as specific as possible :) Much appreciated -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] Re: Best way to handle linear rigid molecules.
M_CO2.top, line 8230]: atom C_CO (Res CO2-1) has mass 0 ERROR 2 [file MCM_CO2.top, line 8230]: atom O_CO (Res CO2-1) has mass 0 ERROR 3 [file MCM_CO2.top, line 8230]: atom O_CO (Res CO2-1) has mass 0 ERROR 4 [file MCM_CO2.top, line 8230]: virtual site DUM (Res CO2-1) has non-zero mass 22.005 Check your topology. ERROR 5 [file MCM_CO2.top, line 8230]: virtual site DUM (Res CO2-1) has non-zero mass 22.005 Check your topology. So the approach of modelling dummy atoms with a mass and the real atoms as mass-less generates errors. How do I solve this? Importantly I need to get the MSD of the CO2 molecules so I am a bit confused with the approach of using virtual atom sites to model CO2. Which groups would I then select for the MSD? The virtual site with the mass or the real atoms site which is mass-less? Is this approach realistic? I have also tried to model CO2 2 different approaches 1. Using bond constraints and setting the bond angle to 180 and using a large bending constant to keep the molecule effectively rigid. Here I got the following error message and the run stopped after 2 timesteps; Step 1, time 0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.969889, max 10.563440 (between atoms 1072 and 1074) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1072 1073 89.90.1210 0.6876 0.1209 1072 1074 92.40.1210 1.3978 0.1209 1075 1076 86.80.1209 0.1303 0.1209 1075 1077 86.80.1209 0.1307 0.1209 Wrote pdb files with previous and current coordinates 2. Using constraints to keep the C-O bond fixed to 0.12 and another constraint between O and O of 0.24. I hoped this would keep the O-C-O linear. Here, the md.log file contained the following; 6 constraints are involved in constraint triangles, will apply an additional matrix expansion of order 4 for couplings between constraints inside triangles The job ran to completion but on viewing the trajectory, the CO2 molecules are only approximately linear. If anyone has an example file for a triatomic linear molecule like CO2, I?d be very grateful if you could post it so I could use it as a template, I am using gromacs version 4.0.5 Thanks Hi, This question has been asked several times before on this list. The proper way to handle this in Gromacs is to introduce two dummy mass particles in such a way the total mass and the moment of inertia is identical to CO2. Then you can construct the positions of the three mass-less C and O atoms from the positions of the masses using virtual sites (see the manual). Berk Quoting Jennifer Williams : > Hello users, > > I am using gromacs v 4.0.5 > > What is the best way to treat linear triatomic molecules such as CO2. > Is there some kind of rigid algorthym as in DL_POLY? > > In the asbsence of a ?rigid? algorthym. I initially intended to ?fix? > the C=O bond length using constraints (as below) and somehow ?fix? the > O=C=O bond angle to 180. > > > [ atomtypes ] > ; type masschargeptype c6c12 >C_CO212.011150.5406 A 0. 0. >O_CO215.9994-0.2703 A 0.29847 1.10765301 > > [ moleculetype ] > ; name nrexcl > CO2 2 > > [ atoms ] > ; nr typeresnr residu atomcgnrcharge mass > 1 C_CO2 1 CO2C_CO2 10.5406 12.01115 > 2 O_CO2 1 CO2O_CO2 1 -0.2703 15.9994 > 3 O_CO2 1 CO2O_CO2 1 -0.2703 15.9994 > > [ constraints ] > ; ai aj funct c0 c1 > 1 2 1 0.12088 > 1 3 1 0.12088 > > [ angles ] > ; aiajak funct c0 c1 > 2 1 3 1 180.00 > > First question... How do I go about fixing this angle to 180degrees? > Should I just make c1 extremely large? Is there a more elegant way of > going about this? Someone also mentioned using a virtual site > representation for the C. Any comments on this welcome. > > I read some posts which imply that the angle bending code apparently can't > handle angles of exactly 180 degrees. > > http://www.mail-archive.com/gmx-users@gromacs.org/msg09979.html > > This was a while ago so perhaps this has been dealt with in the current > version of gromacs? > > > Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don&
[gmx-users] Re: Best way to handle linear rigid molecules.
Hi gmx users I am still having problems modelling small linear molecules. Following advice from the forum (see below), I tried to define CO2 using 2 dummy atoms (with averaged masses) which I placed in the same positions as my oxygen atoms. (This involves having to replicate coordinates for O in my pdb file which will be fiddly when I have hundreds of CO2 molecules). Here is my .itp file for CO2; [ atomtypes ] ; type masschargeptype c6c12 C_CO0.000 0.5406 A 0. 0. O_CO0.000-0.2703 A 0.29847 1.10765301 DUM22.004975 0. V 0. 0. [ moleculetype ] ; name nrexcl CO2 2 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 C_CO 1 CO2C_CO 10.5406 0.000 2 O_CO 1 CO2O_CO 1 -0.2703 0.000 3 O_CO 1 CO2O_CO 1 -0.2703 0.000 4 DUM 1 CO2DUM 10. 22.004975 5 DUM 1 CO2DUM 10. 22.004975 [ constraints ] ; ai aj funct c0 c1 2 3 1 0.24176 [ virtualsites2] ; aiajak funct c0 c1 4 2 3 1 0. 5 2 3 1 0.24176 I am not sure what the final terms in the virtual sites section stand for and I have not found a lot of detail in the manual (section 4.7 and 5.5.2). I assumed that the first term defines the virtual atom site, the second and third are the positions of the real atoms which the virtual atom is placed in relation to. What does the function ?1? stand for? Here I tried to place the virtual atoms in the same positions as my ?real? oxygens- I am not sure if this will be allowed? However, when I run this I get: ERROR 1 [file MCM_CO2.top, line 8230]: atom C_CO (Res CO2-1) has mass 0 ERROR 2 [file MCM_CO2.top, line 8230]: atom O_CO (Res CO2-1) has mass 0 ERROR 3 [file MCM_CO2.top, line 8230]: atom O_CO (Res CO2-1) has mass 0 ERROR 4 [file MCM_CO2.top, line 8230]: virtual site DUM (Res CO2-1) has non-zero mass 22.005 Check your topology. ERROR 5 [file MCM_CO2.top, line 8230]: virtual site DUM (Res CO2-1) has non-zero mass 22.005 Check your topology. So the approach of modelling dummy atoms with a mass and the real atoms as mass-less generates errors. How do I solve this? Importantly I need to get the MSD of the CO2 molecules so I am a bit confused with the approach of using virtual atom sites to model CO2. Which groups would I then select for the MSD? The virtual site with the mass or the real atoms site which is mass-less? Is this approach realistic? I have also tried to model CO2 2 different approaches 1. Using bond constraints and setting the bond angle to 180 and using a large bending constant to keep the molecule effectively rigid. Here I got the following error message and the run stopped after 2 timesteps; Step 1, time 0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.969889, max 10.563440 (between atoms 1072 and 1074) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1072 1073 89.90.1210 0.6876 0.1209 1072 1074 92.40.1210 1.3978 0.1209 1075 1076 86.80.1209 0.1303 0.1209 1075 1077 86.80.1209 0.1307 0.1209 Wrote pdb files with previous and current coordinates 2. Using constraints to keep the C-O bond fixed to 0.12 and another constraint between O and O of 0.24. I hoped this would keep the O-C-O linear. Here, the md.log file contained the following; 6 constraints are involved in constraint triangles, will apply an additional matrix expansion of order 4 for couplings between constraints inside triangles The job ran to completion but on viewing the trajectory, the CO2 molecules are only approximately linear. If anyone has an example file for a triatomic linear molecule like CO2, I?d be very grateful if you could post it so I could use it as a template, I am using gromacs version 4.0.5 Thanks Hi, This question has been asked several times before on this list. The proper way to handle this in Gromacs is to introduce two dummy mass particles in such a way the total mass and the moment of inertia is identical to CO2. Then you can construct the positions of the three mass-less C and O atoms from the positions of the masses using virtual sites (see the manual). Berk Quoting Jennifer Williams : Hello users, I am using gromacs v 4.0.5 What is the best way to treat linear triatomic molecules such as CO2. Is there some kind of rigid algorthym as in DL_POLY? In the asbsence of a ?rigid? algorthym. I initially intended to ?fix? the C=O bond length using constraints (as below) and somehow ?fix? the O=C=O
[gmx-users] Best way to handle linear rigid molecules.
Hello users, I am using gromacs v 4.0.5 What is the best way to treat linear triatomic molecules such as CO2. Is there some kind of rigid algorthym as in DL_POLY? In the asbsence of a ?rigid? algorthym. I initially intended to ?fix? the C=O bond length using constraints (as below) and somehow ?fix? the O=C=O bond angle to 180. [ atomtypes ] ; type masschargeptype c6c12 C_CO212.011150.5406 A 0. 0. O_CO215.9994-0.2703 A 0.29847 1.10765301 [ moleculetype ] ; name nrexcl CO2 2 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 C_CO2 1 CO2C_CO2 10.5406 12.01115 2 O_CO2 1 CO2O_CO2 1 -0.2703 15.9994 3 O_CO2 1 CO2O_CO2 1 -0.2703 15.9994 [ constraints ] ; ai aj funct c0 c1 1 2 1 0.12088 1 3 1 0.12088 [ angles ] ; aiajak funct c0 c1 2 1 3 1 180.00 First question... How do I go about fixing this angle to 180degrees? Should I just make c1 extremely large? Is there a more elegant way of going about this? Someone also mentioned using a virtual site representation for the C. Any comments on this welcome. I read some posts which imply that the angle bending code apparently can't handle angles of exactly 180 degrees. http://www.mail-archive.com/gmx-users@gromacs.org/msg09979.html This was a while ago so perhaps this has been dealt with in the current version of gromacs? Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] pdb2gmx adding a residue to the .rtp file
Hi, I am trying to use the pdb2gmx to generate a .top file from my .pdb. I am getting the following error?. All occupancies are one Opening library file /home/jwillia4/gromacs/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file /home/jwillia4/gromacs/share/gromacs/top/ffoplsaa.rtp Residue 56 --- Program pdb2gmx, VERSION 4.0.5 Source code file: resall.c, line: 138 Fatal error: Atom type opls_23 (residue MCM) not found in atomtype database As my residue is not already present I have added the following to the end of the ffoplsaa.rtp file [ MCM ] [ atoms ] OHopls_23-0.70 1 HOopls_24 0.435 1 SI SI 0.832 1 OSopls_62-0.400 1 [ bonds ] SIOS SIOH OHHO [ dihedrals ] OSSIOHHO SIOSSIOS SIOSSIOH OHSIOHHO The following is already present in the ffoplsaabon.itp file (standard version); ; This bit added by DvdS for quartz simulation 2005-05-07 ; These parameters are taken from GROMOS and were also used in ; Wensink et al. Langmuir 16 (2000) pp. 7392-7400 ; [ bondtypes ] ; ij func b0 kb SIOS 10.16300 251040. ; From GROMACS SIOH 10.16300 251040. ; [ angletypes ] ; ijk func th0 cth SI OS SI1 155.000 397.480 OS SI OS1 109.500 397.480 OH SI OS1 109.500 397.480 SI OH HO1 109.500 397.480 [ dihedraltypes ] ; ijkl func coefficients ; Added DvdS for Quartz simulations SI OS1 0.000 3.766 3 SI OH1 0.000 3.766 3 And the entries in the .atp file which I am getting the error message about are already there (they are in the standard version-I didn?t need to add them myself). So I can?t figure out why they are not being read. I also tried adding the name of my residue (MCM) to aminoacids.dat and incrementing the count at the top. Do I need to make any other changes? Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Why is triclinic geometry not retained in confout.gro?
Hello gmx-users I?m having problems with my mdrun (probably a newbie question). I?m using the latest version of gromacs. I have my .pdb file (or .gro), mdp and .top files ready and can generate the .tpr file. When I run this (with an simple energy minimisation) the simulation runs to completion (I?ve only tried a very short run) but I get a strange confout.gro file as output. My unit cell is triclinic and my input files (both .pdb or .gro) looks fine in VMD. The confgro.out file is strange in that the box has been converted to cubic when I view it in VMD. Is this normal? Why doesn?t it retain the triclinic shape I defined in the pdb file? I?ve been over the topology but my inexperienced eyes can?t see anything wrong. One thing I did notice is that when I looked at the tpr file, all of my atom numbers were shifted by 1 with regards to my topology file i.e In the tpr file, the first angle listed is for atoms 364, 0 and 413 Angle: nr: 9492 iatoms: 0 type=11 (ANGLES) 364 0 413 But in the topology file the first angle I have listed is for 365, 1 and 414. [ angles ] ; ai aj ak funct c0 c1 365 1 414 1 109.04 289.095916 In my pdb and top file my atoms are labelled from 1-1071 whereas in the .tpr file they are labelled from 0-1070. Is this something I should be worried about? Below I have pasted sections of my top file, my pdb file and my .mdp file. I?d appreciate if someone could look over and see that my triclinic unit cell is correctly defined (although the input file looks OK when viewed in VMD). If anyone has the time or inclination to try and run my files (if that helps spot the error), I would be happy to e-mail them and would be very grateful, If you see anything else that looks odd, please feel free to point it out as I am new to gromacs, Thanks in advance, Jenny pdb CRYST1 46.421 43.630 18.960 90.00 90.00 120.00 P 1 1 ATOM 1 SI X 1 -22.104 -1.646 -1.173 1.00 0.00 SI ATOM 2 SI X 1 8.325 -18.877 8.329 1.00 0.00 SI ATOM 3 SI X 1 27.146 -12.854 3.831 1.00 0.00 SI ATOM 4 SI X 1 -14.415 -11.322 4.375 1.00 0.00 SI ATOM 5 SI X 1 -10.624 -15.731 -7.960 1.00 0.00 SI ... ATOM289 O X 1 19.588 -18.099 7.519 1.00 0.00 ATOM290 O X 1 -19.450 0.838 -2.667 1.00 0.00 ... ATOM794 O X 1 22.966 -15.478 -8.908 1.00 0.00 ATOM795 O X 1 17.234 -5.878 -2.785 1.00 0.00 ATOM796 OH X 1 -7.634 -18.464 -3.746 1.00 0.00 ATOM797 H X 1 -7.655 -18.213 -4.662 1.00 0.00 H ATOM798 OH X 1 7.669 -17.509 7.819 1.00 0.00 ATOM799 H X 1 8.061 -17.122 7.046 1.00 0.00 H ATOM 1068 OH X 1 4.808 -14.731 1.210 1.00 0.00 ATOM 1069 H X 1 3.887 -14.515 1.123 1.00 0.00 H ATOM 1070 OH X 1 18.839 0.763 -8.266 1.00 0.00 ATOM 1071 H X 1 18.283 0.835 -9.032 1.00 0.00 H END Topology file [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 1.01.0 ; ; [ atomtypes ] ; typemasschargeptype c6c12 SI 28.08 1.28 A0.000 0.00 O 15.999-0.64 A0.27081.538176 OH 15.999-0.53 A0.30 1.538176 H 1.008 0.21 A0.000 0.000 ; [ moleculetype ] ; Namenrexcl MCM 3 [ atoms ] ; nr typeresnr residue atomcgnrcharge mass 1 SI 1 MCM SI 1 1.2804993 28.086 2 SI 1 MCM SI 2 1.2804993 28.086 3 SI 1 MCM SI 3 1.2804993 28.086 4 SI 1 MCM SI 4 1.2804993 28.086 5 SI 1 MCM SI 5 1.2804993 28.086 ... 289 O 1 MCM O 289 -0.64024965 15.9994 290 O 1 MCM O 290 -0.64024965 15.9994 ... 794 O 1 MCM O 794 -0.64024965 15.9994 795 O 1 MCM O 795 -0.64024965 15.9994 796 OH 1 MCM OH 796 -0.52612471 15.9994 797 H 1 MCM H 797 0.20599988 1.00797 798 OH 1 MCM OH 798 -0.52612471 15.9994 799 H 1 MCM H 799 0.20599988 1.00797 ... 1068
[gmx-users] Conversion of units to nm in .xyz or pdb
hello gromacs users, I am working with a silica structure which is parallepiped in structure, i.e the unit cell is 46.4207 37.7846 18.9596 angles =90, 90, 120 I have a structure file in .xyz and .pdb but the units are in Angstroms and for gromacs I assume that I need to convert these units to nm? This is where I am encountering problems. I have tried simply dividing the atomic coordinates and cell lengths by a factor of 10 but the resulting structure doesnt look right in vmd. Do I need to use some sort of symmetry transformation to take the non-cubic symmetry into account when scaling the coordinates? Is there some program (either within gromacs or external) which will convert atomic coordinates from Angstroms to nm while carrying out the necessary symmetry operations? Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
