[gmx-users] Fatal error during lipid bilayer minimization
Hi I am trying to simulate the self-assembly of course-grained DSPC lipids into a lipid bilayer. I made a box (7.5 x 7.5 x 7.5) containing 128 DSPC lipids, and added 768 molecules of water to the system, and ran a minimization (using em.mdp). The summary of the results is below. Reached the maximum number of steps before reaching Fmax 10 writing lowest energy coordinates. Steepest Descents did not converge to Fmax 10 in 501 steps. Potential Energy = -4.2206562e+04 Maximum force = 4.0814236e+02 on atom 197 Norm of force = 1.2755975e+01 gcq#88: I Don't Want to Catch Anybody Not Drinking. (Monty Python) I also did further minimisations, reducing the max. force to about 29, and the norm of force to about 1.96 For the next step i.e bilayer self-assembly, I ran another minimization (using md.mdp) and I received the following fatal error: Program mdrun, VERSION 4.5.5 Source code file: domdec_top.c, line: 356 Fatal error: 1 of the 2944 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck How should I deal with this? Thanks. -- 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] LINCS warning in md run
On 9/13/12 4:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, this atom is the CG atom of the phosphate I added to the protein. But how can I find out by what it is punished? Visualization. This is the topology for this residue in the aminoacid.rtp file. I added it manually. The parameter are from the amber parameter database (http://www.pharmacy.manchester.ac.uk/bryce/amber/): [ TYP ] [ atoms ] NN -0.5163001 CACT 0.2755032 HAH1 0.0082233 CBCT -0.3540524 HB1HC 0.1103265 HB2HC 0.1103266 CGCA 0.1197287 CD1CA -0.1989388 HD1HA 0.1371439 CE1CA -0.284884 10 HE1HA 0.177179 11 CZC0.452616 12 OHOS -0.534452 13 HH0.293600 14 CE2CA -0.284884 15 HE2HA 0.177179 16 CD2CA -0.198938 17 HD2HA 0.137143 18 CC0.536600 19 OO -0.581900 20 PP1.393213 21 OP1OH -0.752821 22 OP2O2 -0.822464 23 OP3O2 -0.822464 24 H1PHO 0.423316 25 [ bonds ] N H NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZOS CZ CE2 OS P CE2 HE2 CE2 CD2 CD2 HD2 C O -C N P OP1 P OP2 P OP3 OP1 H1P [ impropers ] -CCA N H CA+N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CD1CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2CGCB CE1 CE2CZOH Additionally I had to add an entry in the ffbonded file in the part [ dihedraltypes ] CA CA C OS 4 180.00 4.60240 2; Here I am not completely sure about the entry because I could not find a source for this combination of atoms. But there is already an entry for the combination CA CA C OH Which has the same parameters. Could this be the problem? And if it could be, can you please give me hint where I can find parameters for it? Because I really could not find it. Potentially - if you haphazardly assign parameters, you may get unexpected results. There is a cited reference for the TYP parameters at the website above. I would suggest looking there first, and if there is nothing listed, then contact the corresponding author of the study that first used/derived the parameters. Additionally, if you freeze a part of the protein's structure, you prevent any existing clashes from being resolved. That may be the root of the issue. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Resuming of calculation from last *.cpt
On 9/13/12 1:12 AM, James Starlight wrote: Dear Gromacs Users! I'm looking for possible way to resume trajectory calculations after that calculations have been stoped. Typically in such cases I start new task using cpt file from incomplete run. This produce new trajectory which start from the last frame of previous run. After that I have to merge both files. Is there any way to go on sinulation in the existed files from the last frame of incomplete run without creating of new ones? You can only continue from the last frame if you have a checkpoint file that corresponds to that frame. Use of the -append flag with mdrun will append to existing files rather than creating new ones. This should be default behavior in Gromacs 4.5.x. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS warning in md run
Ah okey. Thank you. I will write them. Hmm, but the protein is a crystal structure from pdb with a resolution of 1.2. I already added the hydrogen atoms to this structure and there I already minimized them and made a md run. And there were no errors. And now I only added the phosphate to the minimized structure. So I thought that I only had to minimize the phosphate and the residue it bound on. Or is there a mistake in my thought here? On 9/13/12 4:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, this atom is the CG atom of the phosphate I added to the protein. But how can I find out by what it is punished? Visualization. This is the topology for this residue in the aminoacid.rtp file. I added it manually. The parameter are from the amber parameter database (http://www.pharmacy.manchester.ac.uk/bryce/amber/): [ TYP ] [ atoms ] NN -0.5163001 CACT 0.2755032 HAH1 0.0082233 CBCT -0.3540524 HB1HC 0.1103265 HB2HC 0.1103266 CGCA 0.1197287 CD1CA -0.1989388 HD1HA 0.1371439 CE1CA -0.284884 10 HE1HA 0.177179 11 CZC0.452616 12 OHOS -0.534452 13 HH0.293600 14 CE2CA -0.284884 15 HE2HA 0.177179 16 CD2CA -0.198938 17 HD2HA 0.137143 18 CC0.536600 19 OO -0.581900 20 PP1.393213 21 OP1OH -0.752821 22 OP2O2 -0.822464 23 OP3O2 -0.822464 24 H1PHO 0.423316 25 [ bonds ] N H NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZOS CZ CE2 OS P CE2 HE2 CE2 CD2 CD2 HD2 C O -C N P OP1 P OP2 P OP3 OP1 H1P [ impropers ] -CCA N H CA+N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CD1CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2CGCB CE1 CE2CZOH Additionally I had to add an entry in the ffbonded file in the part [ dihedraltypes ] CA CA C OS 4 180.00 4.60240 2; Here I am not completely sure about the entry because I could not find a source for this combination of atoms. But there is already an entry for the combination CA CA C OH Which has the same parameters. Could this be the problem? And if it could be, can you please give me hint where I can find parameters for it? Because I really could not find it. Potentially - if you haphazardly assign parameters, you may get unexpected results. There is a cited reference for the TYP parameters at the website above. I would suggest looking there first, and if there is nothing listed, then contact the corresponding author of the study that first used/derived the parameters. Additionally, if you freeze a part of the protein's structure, you prevent any existing clashes from being resolved. That may be the root of the issue. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] LINCS warning in md run
On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Ah okey. Thank you. I will write them. Hmm, but the protein is a crystal structure from pdb with a resolution of 1.2. I already added the hydrogen atoms to this structure and there I already minimized them and made a md run. And there were no errors. And now I only added the phosphate to the minimized structure. So I thought that I only had to minimize the phosphate and the residue it bound on. Or is there a mistake in my thought here? If adding the phosphate resulted in a crash, then clearly that's the problem. I don't understand why you would run EM on just the phosphate and keep the rest of the protein structure frozen. Again, that potentially prevents clashes from being resolved. I don't understand what value there is in only minimizing the phosphate. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_covar -reg
Respected Sir / Madam i did temperature study for that i need analysis principal component analysis so, i followed GROMACS Introductory Tutorial (4.5.5) *g_covar* g_covar -s md_0_2.tpr -f md_merged_20_ns.xtc -o 2KW8_275_eigenval.xvg -v 2KW8_275_eigenvect.trr -xpma 2KW8_275_covara.xpm Choose a group for the least squares fit: 4(Backbone) Choose a group for the least squares fit: 4(Backbone) *xpm2ps* xpm2ps -f 2KW8_275_covara.xpm -o 2KW8_275_covara.eps -do covara.m2p in all my result nothing is there visualize, color is very poor to understand what can i do? kindly give me prompt answer Thanking You In Advance -- *S.VENKATESH* -- 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] Resuming of calculation from last *.cpt
Justin, I've used grompp -f md_sd.mdp -c start.gro -t incomplete.cpt -p topol.top -o incomplete.tpr mpiexec -np 48 mdrun_mpi.openmpi -v -deffnm incomplete -append where incomplete.cpt was checkpoint from previous run and -o incomplete.tpr was the name for new trajectory (in that case its equal to the name of old trajectory ) that produce new .trr .edr and other files and back up old ( e.g crete #incomplete.trr etc) ones instead of continuation of the existing ( incomplete ) trajectory What I've done wrong? 2012/9/13, Justin Lemkul jalem...@vt.edu: On 9/13/12 1:12 AM, James Starlight wrote: Dear Gromacs Users! I'm looking for possible way to resume trajectory calculations after that calculations have been stoped. Typically in such cases I start new task using cpt file from incomplete run. This produce new trajectory which start from the last frame of previous run. After that I have to merge both files. Is there any way to go on sinulation in the existed files from the last frame of incomplete run without creating of new ones? You can only continue from the last frame if you have a checkpoint file that corresponds to that frame. Use of the -append flag with mdrun will append to existing files rather than creating new ones. This should be default behavior in Gromacs 4.5.x. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Resuming of calculation from last *.cpt
On 9/13/12 9:56 AM, James Starlight wrote: Justin, I've used grompp -f md_sd.mdp -c start.gro -t incomplete.cpt -p topol.top -o incomplete.tpr mpiexec -np 48 mdrun_mpi.openmpi -v -deffnm incomplete -append where incomplete.cpt was checkpoint from previous run and -o incomplete.tpr was the name for new trajectory (in that case its equal to the name of old trajectory ) that produce new .trr .edr and other files and back up old ( e.g crete #incomplete.trr etc) ones instead of continuation of the existing ( incomplete ) trajectory What I've done wrong? You shouldn't be invoking grompp at all. http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#Version_4.x -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Charmm for Proteins
Dear All, Could you please write me which is the latest version of Charmm force field for proteins? I want to study protein folding in explicit solvent. Is it available in Gromacs? Steven -- 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] Charmm for Proteins
charmm27 is the canonical charmm protein FF, which is supported by gromacs. Note that if you are using gromacs prior to 4.5.5 to use -nochargegrp when using pdb2gmx when parameterizing your protein. On 2012-09-13 04:19:16PM +0100, Steven Neumann wrote: Dear All, Could you please write me which is the latest version of Charmm force field for proteins? I want to study protein folding in explicit solvent. Is it available in Gromacs? Steven -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Reg pdb2gmx for Cyclic peptide
Dear Justin Thank you for your Previous reply, sorry for the inconvenience to you personal Mail. I am doing MD Cyclic Peptide When I run pdb2gmx , The Conect Infromation in pdb file are ignored . so that it is not able to connect the first and last residue in cycle . But it construct and .top and.gro files successfully while in .gro file the end residues are closed as NH3+ and COO-(charge) (it means there is Bond between Nitrogen and carbon atom) It consider the N atom of first residue as NH3+ and C atom as COO-(charge) but I need to take N as peptide Nitrogen and C as Peptide carbon What Should i do to invoke conect information when i run pdb2gmx tool Also Can i Directly Edit (it means removing excess hydrogen and oxygen atom by ; symbol) .top an .gro files and can i use to proceed further ? Thanks in Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reg pdb2gmx for Cyclic peptide
On 9/13/12 11:42 AM, vidhya sankar wrote: Dear Justin Thank you for your Previous reply, sorry for the inconvenience to you personal Mail. I am doing MD Cyclic Peptide When I run pdb2gmx , The Conect Infromation in pdb file are ignored . so that it is not able to connect the first and last residue in cycle . But it construct and .top and.gro files successfully while in .gro file the end residues are closed as NH3+ and COO-(charge) (it means there is Bond between Nitrogen and carbon atom) It consider the N atom of first residue as NH3+and C atom as COO-(charge) but I need to take N as peptide Nitrogen and C as Peptide carbon What Should i do to invoke conect information when i run pdb2gmx tool Use the -ter option and choose None for both termini. Also Can i Directly Edit (it means removing excess hydrogen and oxygen atom by ; symbol) .top an .gro files and can i use to proceed further ? No. This will cause errors in the [moleculetype] numbering and all successive directives. Re-run pdb2gmx instead. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] .xtc support in UCSF Chimera
Thought people might want to know that thanks to the XTC Library, Chimera now support reading trajectories where the coordinates are in .xtc format. That support is only in the daily build of Chimera, not the production release. www.cgl.ucsf.edu/chimera --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -- 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] CfP: 3rd International Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim13) part of the Symposium on Theory of Modeling and Simulation SCS SpringSim 2013)
# CALL FOR PAPERS 3rd International Workshop on Model-driven Approaches for Simulation Engineering part of the Symposium on Theory of Modeling and Simulation (SCS SpringSim 2013) # April 7-10, 2013, San Diego, CA (USA) http://www.sel.uniroma2.it/Mod4Sim13 # # Papers Due: *** November 1, 2012 *** # Accepted papers will be published in the conference proceedings # and archived in the ACM Digital Library. # The workshop aims to bring together experts in model-based, model-driven and software engineering with experts in simulation methods and simulation practitioners, with the objective to advance the state of the art in model-driven simulation engineering. Model-driven engineering approaches provide considerable advantages to software systems engineering activities through the provision of consistent and coherent models at different abstraction levels. As these models are in a machine readable form, model-driven engineering approaches can also support the exploitation of computing capabilities for model reuse, programming code generation, and model checking, for example. The definition of a simulation model, its software implementation and its execution platform form what is known as simulation engineering. As simulation systems are mainly based on software, these systems can similarly benefit from model-driven approaches to support automatic software generation, enhance software quality, and reduce costs, development effort and time-to-market. Similarly to systems and software engineering, simulation engineering can exploit the capabilities of model-driven approaches by increasing the abstraction level in simulation model specifications and by automating the derivation of simulator code. Further advantages can be gained by using modeling languages, such as UML and SysML – but not exclusively those. For example, modeling languages can be used for descriptive modeling (to describe the system to be simulated), for analytical modeling (to specify analytically the simulation of the same system), and for implementation modeling (to define the respective simulator). A partial list of topics of interest includes: * model-driven simulation engineering processes * requirements modeling for simulation * domain specific languages for modeling and simulation * model transformations for simulation model building * model transformations for simulation model implementation * model-driven engineering of distributed simulation systems * relationship between metamodeling standards (e.g., MOF, Ecore) and distributed simulation standards (e.g., HLA, DIS) * metamodels for simulation reuse and interoperability * model-driven technologies for different simulation paradigms (discrete event simulation, multi-agent simulation, sketch-based * simulation, etc.) * model-driven methods and tools for performance engineering of simulation systems * simulation tools for model-driven software performance engineering * model-driven technologies for simulation verification and validation * model-driven technologies for data collection and analysis * model-driven technologies for simulation visualization * Executable UML * Executable Architectures * SysML / Modelica integration * Simulation Model Portability and reuse * model-based systems verification and validation * simulation for model-based systems engineering To stimulate creativity, however, the workshop maintains a wider scope and welcomes contributions offering original perspectives on model-driven engineering of simulation systems. +++ On-Line Submissions and Publication +++ We invite paper submissions in three forms: 1. Full paper (max 8 pages), describing innovative research results. These papers are eligible for the best paper award and may be invited for an extended version in a special issue of the SCS SIMULATION journal. 2. Work-in-progress paper (max 6 pages), describing novel research ideas and promising work that have not yet been fully evaluated. 3. Short paper (max 6 pages), describing industrial and hands-on experience on any relevant area (i.e. military, government, space, etc.). All the papers must be submitted through the SCS conference management systems (http://www.softconf.com/scs/DEVS13/) and select the Mod4Sim track. The submissions must be in PDF format and conform to the SCS conference template (Word template is available at http://www.scs.org/upload/documents/templates/ConferenceSubmissionWORDTemplate.doc , guidelines are available at http://www.scs.org/PDFs/formattingkit.pdf). All the submitted papers must be original and not submitted else where. Submitted papers
[gmx-users] Segmentation fault (core dumped error)
Dear all, I am trying to study the MD of a Carbon Nanotube interacting with some polymers. and I have some problems in forming the topology files. I have actually two questions and I hope you can help me in that. (1) In an attempt to form the topology files of CNTs and graphene (using x2top), i have found on the internet scripts (by Andrea Minoia I guess). These constitute of adding .nt2, .rtp. and .itp files to the /Gromacs/share/Gromacs/top directory (namely ffcntoplsaa.nt2, ffcntoplsaa.rtp and ffcntoplsaa.itp) and adding a line in the FF.dat file. I have done that and tried to execute x2top and I got the error: ..Entries in elements.dat: 218Looking whether force field files existOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.rtpOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tThere are 0 name to type translationsGenerating bonds from distances...Segmentation fault (core dumped) Can anyone please tell me the source of this error and how to fix it? (2) I will definitely need a top file for the polymers I will also be solvating. But I also have problems because the pdb file contains a LIG residue unrecognizable by Gromacs. I have asked this question before and I was advised to change some files accordingly but to be honest I am not really professional in that; I have asked someone who had a problem in the past but he did not know all the details because he ended up not using the modified force fields after all. Can anyone give me in details how to incorporate the residue LIG within the force field or let me know whom I can consult...A part of the pdb file with the residue LIG is: COMPNDUNNAMEDAUTHORGENERATED BY OPEN BABEL 2.3.1HETATM1 C LIG 1 1.481 -1.276 -0.621 1.00 0.00 CHETATM2 C LIG 1 2.216 -2.370 -1.040 1.00 0.00 CHETATM3 S LIG 1 3.770 -2.409 -0.306 1.00 0.00 SHETATM4 C LIG 1 3.456 -0.998 0.609 1.00 0.00 CHETATM5 C LIG 1 2.207 -0.479 0.313 1.00 0.00 CHETATM6 C LIG 1 5.156 0.676 1.386 1.00 0.00 CHETATM7 C LIG 1 4.423 -0.491 1.600 1.00 0.00 CHETATM8 C LIG 1 4.550 -1.119 2.847 1.00 0.00 CHETATM9 C LIG 1 5.256 -0.503 3.905 1.00 0.00 CHETATM 10 C LIG 1 6.107 0.592 3.667 1.00 0.00 CHETATM 11 C LIG 1 6.008 1.181 2.393 1.00 0.00 CHETATM 12 S LIG 1 7.457 2.548 5.198 1.00 0.00 SHETATM 13 C LIG 1 7.220 0.945 4.621 1.00 0.00... I am really thankful Elie -- 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
