Hi Justin, I am using the ffoplsaabon.itp parameters for: bonds (CA-CA, CA-CT, CA-HA, CT-HC, H-N3) angles (CA-CA-CA, CA-CA-HA, CA-CT-HC, H-N3-H) dihedrals (X-CA-CA-X, X-CA-CT-X)
I am using the ffolpsaanb.itp VdW parameters for H & N3 And I am using the VdW parameters found in the paper "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules" for CA, HA, CT, & HC doing the conversion from Angstroms (paper units) to nm (ffoplsaanb.itp units) for sigma and from kcal/mol (paper units) to kJ/mol (ffoplsaanb.itp units) for epsilon. The converted parameters for sigma were different by only +/-2% to +/-8% from the values in ffoplsaanb.itp, but the converted parameters for epsilon were different by +/-23% to +/-66% from the values in ffoplsaanb.itp. Is this a valid paper to use for selection of parameters? The graphene lattice is only vibrating slightly and looks like a bunch of travelling waves. I believe I am using proper dihedrals and not improper dihedrals in my model. Since the graphene structure will be connected to electrodes at both ends and will be mounted above a substrate, I assume the atoms in the structure are not completely free and thus I need to model them being restricted in their movement. Maybe position restraints are more appropriate than freezing to model such a situation. I do not see anything in the trajectory that provides clues as to what might be causing the segmentation fault. Thanks again for your help. Darrell >Date: Fri, 17 Jul 2009 19:08:38 -0400 >From: "Justin A. Lemkul" <jalem...@vt.edu> >Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <4a610476.2090...@vt.edu> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > >darre...@ece.ubc.ca wrote: >> Hi Justin, >> I froze the graphene sheet because, prior to freezing it, I noticed that >> it was vibrating and thought that maybe its vibration was not allowing >> the NH3 molecules to adsorb (bond) to it. But after freezing the >> graphene sheet, I see that see that NH3 molecules are still not bonding >> to it. Physical experiments of NH3 and a graphene lattice connected to >> electrodes have shown that NH3 does adsorb to graphene, but all I see >> are NH3 molecules coming close to the graphene surface and then bouncing >> away which I am assuming is a result of repulsion between the negatively >> charged N atom in the ammonia molecule and the pi electrons in the >> graphene lattice. So I am not sure why experiments have shown adsorption >> unless adsoption is occurring as a result of a current flowing through >> the graphene structure or as a result of edge effects at the interface >> between the electrodes and the graphene lattice. >> > >What parameters are you using for the species involved? Could be that there's >something wrong with your model. > >> Could you tell me how freezing is different that position restraining as >> this is not completely clear to me? >> > >Freezing means positions are absolutely fixed and never updated. Position >restraining means there is an energy penalty to movement, but positions can >adjust slightly. I was thinking that if you have some strange interaction >happening, and freezing was preventing any reaction to the force, then you'd >see >an explosion. I don't necessarily see why you need to apply either, but that >will depend on the extent of "vibration" that you see in the graphene sheet. >Are you applying improper dihedrals appropriately? Are the rings puckering, or >just vibrating slightly (which could be normal)? > >> I will try position restraining the graphene structure and see if that >> resolves my problem. >> >> I have been able to view a trajectory for simulations of fewer than >> 20,000 time steps and see the frozen graphene lattice and the NH3 >> molecules floating through space. >> >> Note that the segmentation fault only occurs sometime between 20,000 and >> 30,000 time steps. Could it be that the "funky" behaviour associated >> with freezing would take 20,000+ time steps to cause a segmentation >> fault? >> > >Depends entirely upon what's causing the explosion. Any clues from the >trajectory? > >-Justin > >> Thanks again for your help. >> >> Darrell >> >>> Date: Thu, 16 Jul 2009 16:20:04 -0400 >>> From: "Justin A. Lemkul" <jalem...@vt.edu> >>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) >>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>> Message-ID: <4a5f8b74.6070...@vt.edu> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> >>> >>> darre...@ece.ubc.ca wrote: >>>> Hi Justin, >>>> Thanks for the explanation of the difference between EM & equilibration. >>>> Since in my model, I: (i) only have the graphene sheet and ammonia >>>> molecules spaced reasonably far apart from each other (1332 NH3 >>>> molecules in a 38x38x38 box) and from the graphene sheet (distance >>>> between the closest ammonia molecule and the graphene sheet is greater >>>> than the molecular diameter of ammonia - maybe this is too close and >>>> could be causing my problem?); (ii) freeze the graphene sheet; I am >>>> thinking equilibration is not required in my model. Please let me know >>>> if you think I still need to perform equilibration. >>>> >>>> Yes, the EM did converge satisfactorily. Here is the output from EM: >>>> Steepest Descents converged to Fmax < 250 in 61 steps >>>> Potential Energy = 4.6094102e+04 >>>> Maximum force = 2.4543298e+02 on atom 1 >>>> Norm of force = 7.5803179e+03 >>>> >>>> Is this a reasonable value for FMax? >>>> >>> Your Fmax looks fine. Why is it necessary to freeze the graphene sheet? >>> Why >>> not use position restraints (to rule out funky behavior of being frozen)? >>> >>> Did you ever obtain a trajectory with enough frames that you could watch? >>> What >>> happened? >>> >>> -Justin >>> >>>> Thanks again for your help. >>>> >>>> Darrell >>>> >>>> >>>>> Date: Thu, 16 Jul 2009 07:15:12 -0400 >>>>> From: "Justin A. Lemkul" <jalem...@vt.edu> >>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) >>>>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>>>> Message-ID: <4a5f0bc0.4020...@vt.edu> >>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>>> >>>>> >>>>> >>>>> darre...@ece.ubc.ca wrote: >>>>>> Hi Mark, >>>>>> I do not do any equilibration, I only do energy minimization as in the >>>>>> "GROMACS Tutorial for Solvation Study of Spider Toxin Peptide". Please >>>>>> let me know if I need to do equilibration and what is the difference >>>>>> between energy minimization and equilibration as this is not clear to me. >>>>>> >>>>> Did the EM converge satisfactorily? What was Fmax? >>>>> >>>>> Unlike EM, equilibration is an MD process; for a protein system, one >>>>> generally >>>>> position-restrains the protein and allows the surrounding solvent to >>>>> optimize >>>>> around the structure. >>>>> >>>>> -Justin >>>>> >>>>>> Here is an mdp file for a run that actually completed successfully: >>>>>> title =Graphene >>>>>> ;warnings =10 >>>>>> cpp =cpp >>>>>> ;define =-DPOSRES >>>>>> constraints =none >>>>>> integrator =md >>>>>> dt =0.002 ; ps >>>>>> nsteps =10000 >>>>>> nstcomm =100 >>>>>> nstxout =100 >>>>>> ;nstvout =1000 >>>>>> nstfout =0 >>>>>> nstlog =100 >>>>>> nstenergy =100 >>>>>> nstlist =100 >>>>>> ns_type =grid >>>>>> rlist =2.0 >>>>>> coulombtype =PME >>>>>> rcoulomb =2.0 >>>>>> vdwtype =cut-off >>>>>> rvdw =5.0 >>>>>> fourierspacing =0.12 >>>>>> fourier_nx =0 >>>>>> fourier_ny =0 >>>>>> fourier_nz =0 >>>>>> pme_order =4 >>>>>> ewald_rtol =1e-5 >>>>>> optimize_fft =yes >>>>>> >>>>>> ; This section freezes graphene lattice >>>>>> energygrps = Grph NH3 >>>>>> energygrp_excl = Grph Grph >>>>>> freezegrps = Grph ; Freeze graphene lattice >>>>>> freezedim = Y Y Y; in all directions >>>>>> >>>>>> Tcoupl =berendsen >>>>>> tau_t =0.5 0.5 >>>>>> tc-grps =NH3 Grph >>>>>> ref_t =300 300 >>>>>> >>>>>> ;coupl = parrinello-rahman >>>>>> ;tau_p = 1.5 >>>>>> ;compressibility = 1.3 >>>>>> ;ref_p = 0.061 >>>>>> >>>>>> gen_vel = yes >>>>>> gen_temp = 300.0 >>>>>> gen_seed = 173529 >>>>>> >>>>>> And here is a copy of an mdp file for a run that did not complete >>>>>> successfully: >>>>>> >>>>>> title =Graphene >>>>>> ;warnings =10 >>>>>> cpp =cpp >>>>>> ;define =-DPOSRES >>>>>> constraints =none >>>>>> integrator =md >>>>>> dt =0.002 ; ps >>>>>> nsteps =30000 >>>>>> nstcomm =500 >>>>>> nstxout =500 >>>>>> ;nstvout =1000 >>>>>> nstfout =0 >>>>>> nstlog =500 >>>>>> nstenergy =500 >>>>>> nstlist =500 >>>>>> ns_type =grid >>>>>> rlist =2.0 >>>>>> coulombtype =PME >>>>>> rcoulomb =2.0 >>>>>> vdwtype =cut-off >>>>>> rvdw =5.0 >>>>>> fourierspacing =0.12 >>>>>> fourier_nx =0 >>>>>> fourier_ny =0 >>>>>> fourier_nz =0 >>>>>> pme_order =4 >>>>>> ewald_rtol =1e-5 >>>>>> optimize_fft =yes >>>>>> >>>>>> ; This section freezes graphene lattice >>>>>> energygrps = Grph NH3 >>>>>> energygrp_excl = Grph Grph >>>>>> freezegrps = Grph ; Freeze graphene lattice >>>>>> freezedim = Y Y Y; in all directions >>>>>> >>>>>> Tcoupl =berendsen >>>>>> tau_t =0.5 0.5 >>>>>> tc-grps =NH3 Grph >>>>>> ref_t =300 300 >>>>>> >>>>>> ;coupl = parrinello-rahman >>>>>> ;tau_p = 1.5 >>>>>> ;compressibility = 1.3 >>>>>> ;ref_p = 0.061 >>>>>> >>>>>> gen_vel = yes >>>>>> gen_temp = 300.0 >>>>>> gen_seed = 173529 >>>>>> >>>>>> Please let me know what you think might be the problem. >>>>>> >>>>>> Thanks >>>>>> >>>>>> Darrell >>>>>> >>>>>>> Date: Thu, 16 Jul 2009 09:47:49 +1000 >>>>>>> From: Mark Abraham <mark.abra...@anu.edu.au> >>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) >>>>>>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>>>>>> Message-ID: <4a5e6aa5.4040...@anu.edu.au> >>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>>>>> >>>>>>> darre...@ece.ubc.ca wrote: >>>>>>>> Hi Mark, >>>>>>>> Yes, I know that the box dimensions are defined in the last line of the >>>>>>>> .gro file and I have defined these dimensions as 38 nm x 38 nm x 38 nm >>>>>>>> in the .gro file. >>>>>>> OK. >>>>>>> >>>>>>>> I looked through my .gro file to ensure none of the atoms had >>>>>>>> coordinates >>>>>>>> outside the 38x38x38 box. While I was reviewing the file I did notice >>>>>>>> that some coordinates had negative values, slightly negative, but >>>>>>>> negative none the less. Could this be causing the segmentation fault >>>>>>>> between time step 10,000 and time step 30,000? Why wouldn't the >>>>>>>> negative coordinates cause a segmentation fault much earlier? >>>>>>> The absolute value of the coordinates is irrelevant. >>>>>>> >>>>>>> Your choice of 2.0 for rcoulomb is likely suboptimal for PME. Some >>>>>>> smaller value is probably more efficient, but this will not be the cause >>>>>>> of your problem. >>>>>>> >>>>>>> What is your system preparation regime? (i.e. EM + equilibration) >>>>>>> >>>>>>> Can you post a corrected and current .mdp file? >>>>>>> >>>>>>> Mark >>>>>>> >>>>>>>>> Date: Wed, 15 Jul 2009 16:59:21 +1000 >>>>>>>>> From: Mark Abraham <mark.abra...@anu.edu.au> >>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) >>>>>>>>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>>>>>>>> Message-ID: <4a5d7e49.9020...@anu.edu.au> >>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>>>>>>> >>>>>>>>> darre...@ece.ubc.ca wrote: >>>>>>>>>> Hi Justin, >>>>>>>>>> I was experiencing the problem before someone suggested using >>>>>>>>>> editconf so >>>>>>>>>> I do not think the problem is being caused by editconf. But anyway >>>>>>>>>> here >>>>>>>>>> is my editconf command. Let me know if you a source of error in this >>>>>>>>>> command line. >>>>>>>>>> >>>>>>>>>> editconf -f graphene.gro -n index.ndx -o graphene_ec.gro >>>>>>>>>> >>>>>>>>>> I did not want to add in additional space between the solvent and >>>>>>>>>> the box >>>>>>>>>> as I saw no reason for doing so. And hence that is why I originally >>>>>>>>>> did >>>>>>>>>> not use editconf. >>>>>>>>>> >>>>>>>>>> My box dimensions are 38nm x 38nm x 38nm. >>>>>>>>> The box dimensions are defined in the bottom line of the .gro file, >>>>>>>>> and >>>>>>>>> not by the positions of the atoms in that file. If you haven't ever >>>>>>>>> set >>>>>>>>> them to be suitable for your coordinates with editconf, then they >>>>>>>>> might >>>>>>>>> not be. >>>>>>>>> >>>>>>>>> Mark >>>>>>>>> >>>>>>>>> I used cutoffs of 2 nm & 5 nm >>>>>>>>>> for my system so ensure the cutoff occured at a distance where the >>>>>>>>>> potentials were stabalized (not changing). I guess I could use >>>>>>>>>> shorter >>>>>>>>>> cutoffs such as 1.5 nm & 2 nm and this may decrease my computation >>>>>>>>>> time. >>>>>>>>>> I also thought that I needed to use larger cut-offs since I am >>>>>>>>>> dealing >>>>>>>>>> in the gas phase and there is greater ditance between the atoms in my >>>>>>>>>> simulation than in liquid-based simulations. >>>>>>>>>> >>>>>>>>>> In the .log files, I do not see any LINCS warnings or neighborlist >>>>>>>>>> errors. >>>>>>>>>> >>>>>>>>>> I ran gmxcheck on a .trr file and was presented with the following >>>>>>>>>> output: >>>>>>>>>> ********************************************* >>>>>>>>>> Checking file mdtraj.trr >>>>>>>>>> trn version: GMX_trn_file (single precision) >>>>>>>>>> Reading frame 0 time 0.000 >>>>>>>>>> # Atoms 10482 >>>>>>>>>> Last frame 5 time 1.000 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Item #frames Timestep (ps) >>>>>>>>>> Step 6 0.2 >>>>>>>>>> Time 6 0.2 >>>>>>>>>> Lambda 6 0.2 >>>>>>>>>> Coords 6 0.2 >>>>>>>>>> Velocities 6 0.2 >>>>>>>>>> Forces 0 >>>>>>>>>> Box 6 0.2 >>>>>>>>>> ********************************************* >>>>>>>>>> >>>>>>>>>> I ran two additional simulations with different values for nsteps and >>>>>>>>>> nstxxxx paramaters and have the following to report: >>>>>>>>>> >>>>>>>>>> When I run a simulation with the following parameters it completes >>>>>>>>>> successfully and I see, in the log file, the system output every 100 >>>>>>>>>> time steps. >>>>>>>>>> nsteps =10000 >>>>>>>>>> nstcomm =100 >>>>>>>>>> nstxout =100 >>>>>>>>>> nstfout =0 >>>>>>>>>> nstlog =100 >>>>>>>>>> nstenergy =100 >>>>>>>>>> nstlist =100 >>>>>>>>>> >>>>>>>>>> When I run a simulation with the following parameters it fails with a >>>>>>>>>> sementation fault and, in the log file, I do not see system output >>>>>>>>>> every >>>>>>>>>> 500 time steps. >>>>>>>>>> nsteps =30000 >>>>>>>>>> nstcomm =500 >>>>>>>>>> nstxout =500 >>>>>>>>>> nstfout =0 >>>>>>>>>> nstlog =500 >>>>>>>>>> nstenergy =500 >>>>>>>>>> nstlist =500 >>>>>>>>>> >>>>>>>>>> Please let me know what you think might be the problem. >>>>>>>>>> >>>>>>>>>> Thank you very much. >>>>>>>>>> >>>>>>>>>> Darrell >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> Date: Mon, 13 Jul 2009 15:37:15 -0400 >>>>>>>>>>> From: "Justin A. Lemkul" <jalem...@vt.edu> >>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) >>>>>>>>>>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>>>>>>>>>> Message-ID: <4a5b8ceb.4020...@vt.edu> >>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> darre...@ece.ubc.ca wrote: >>>>>>>>>>>> Hi Mark, >>>>>>>>>>>> I used editconf on my .gro file with zero space between my solvent >>>>>>>>>>>> and >>>>>>>>>>>> the box and the resulting box had the exact same dimension as the >>>>>>>>>>>> initial box. I also performed a number of simulation runs with >>>>>>>>>>>> different >>>>>>>>>>> If you're using editconf to define zero space, what's the point? I >>>>>>>>>>> only ask >>>>>>>>>>> because it is a potential source of error if you think you're >>>>>>>>>>> adding zero space, >>>>>>>>>>> but something else might be going on. Maybe you can post your >>>>>>>>>>> editconf command >>>>>>>>>>> line. >>>>>>>>>>> >>>>>>>>>>> What are your box dimensions? Are cut-off lengths of 2.0 and 5.0 >>>>>>>>>>> nm appropriate >>>>>>>>>>> for your system? How did you determine that these cut-off's should >>>>>>>>>>> be used? >>>>>>>>>>> >>>>>>>>>>>> mdp parameters hoping this would provide me some indication of the >>>>>>>>>>>> cause >>>>>>>>>>>> of the fault but to no avail. I looked through the log files, error >>>>>>>>>>>> files, and output files and could not find any output to help me >>>>>>>>>>>> identify the source of my error. >>>>>>>>>>>> >>>>>>>>>>> It is very odd that Gromacs isn't report anything at all. No LINCS >>>>>>>>>>> warnings? >>>>>>>>>>> No neighborlist errors? These would be in the .log file. >>>>>>>>>>> >>>>>>>>>>>> Could you please let me know how I can look at my structure at >>>>>>>>>>>> each point >>>>>>>>>>>> as you indicate below as I do not see any files output that >>>>>>>>>>>> provide me >>>>>>>>>>>> to do so? I tried to look at the .trr file but when I try to load >>>>>>>>>>>> it >>>>>>>>>>>> into VMD, it causes an error. I am assuming this error is caused >>>>>>>>>>>> because >>>>>>>>>>>> the .trr file did not complete correctly due to the segmentation >>>>>>>>>>>> fault. >>>>>>>>>>>> Please advise. >>>>>>>>>>>> >>>>>>>>>>> How early is the segmentation fault occurring? I have found it >>>>>>>>>>> useful sometimes >>>>>>>>>>> to set nstxout (or nstxtcout) = 1 to try to catch the first few >>>>>>>>>>> frames if the >>>>>>>>>>> explosion is occurring early. In any case, gmxcheck will help >>>>>>>>>>> determine how >>>>>>>>>>> many frames are present, as well as the integrity of the file >>>>>>>>>>> (broken frames, etc). >>>>>>>>>>> >>>>>>>>>>> -Justin >>>>>>>>>>> >>>>>>>>>>>> Thanks. >>>>>>>>>>>> >>>>>>>>>>>> Darrell >>>>>>>>>>>> >>>>>>>>>>>>> Date: Tue, 07 Jul 2009 09:19:42 +1000 >>>>>>>>>>>>> From: Mark Abraham <mark.abra...@anu.edu.au> >>>>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) >>>>>>>>>>>>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>>>>>>>>>>>> Message-ID: <4a52868e.6010...@anu.edu.au> >>>>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>>>>>>>>>>> >>>>>>>>>>>>> darre...@ece.ubc.ca wrote: >>>>>>>>>>>>>> Hi Mark, >>>>>>>>>>>>>> I added the energy group exclusions as indicated in your previous >>>>>>>>>>>>>> response but am still experiencing the same problem. I looked at >>>>>>>>>>>>>> the >>>>>>>>>>>>>> .log files and see that in one log file it tells me that my box >>>>>>>>>>>>>> is >>>>>>>>>>>>>> exploding. However, I do not have many molecules in my >>>>>>>>>>>>>> simulation and >>>>>>>>>>>>>> therefore do not think that it is possible that my box is >>>>>>>>>>>>>> exploding from >>>>>>>>>>>>>> pressure. >>>>>>>>>>>>> Sure, but if there's something malformed with your model physics >>>>>>>>>>>>> or >>>>>>>>>>>>> starting configuration, then large forces can make anything >>>>>>>>>>>>> explode. >>>>>>>>>>>>> >>>>>>>>>>>>> Look at your structures at each point and see where things start >>>>>>>>>>>>> to go >>>>>>>>>>>>> wrong. Make sure you've used editconf on your starting structure >>>>>>>>>>>>> to >>>>>>>>>>>>> provide the right box dimensions. >>>>>>>>>>>>> >>>>>>>>>>>>> Mark >>>>>>>>>>>>> >>>>>>>>>>>>>> Maybe if I re-state my simulation it will help you in providing >>>>>>>>>>>>>> me >>>>>>>>>>>>>> direction on what might be causing the problem. My simulation >>>>>>>>>>>>>> consists >>>>>>>>>>>>>> of a graphene lattice with a layer of ammonia molecules above >>>>>>>>>>>>>> it. The >>>>>>>>>>>>>> box is very large and there is lots of empty space in the box. >>>>>>>>>>>>>> So I am a >>>>>>>>>>>>>> little confused as to how the box could be exploding. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks again in advance for your help. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Darrell Koskinen >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Date: Fri, 03 Jul 2009 11:41:45 +1000 >>>>>>>>>>>>>>> From: Mark Abraham <mark.abra...@anu.edu.au> >>>>>>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) >>>>>>>>>>>>>>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>>>>>>>>>>>>>> Message-ID: <4a4d61d9.6080...@anu.edu.au> >>>>>>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> darre...@ece.ubc.ca wrote: >>>>>>>>>>>>>>>> Dear GROMACS Gurus, >>>>>>>>>>>>>>>> I am experiencing a segmentation fault when mdrun executes. My >>>>>>>>>>>>>>>> simulation >>>>>>>>>>>>>>>> has a graphene lattice with an array (layer) of ammonia >>>>>>>>>>>>>>>> molecules above >>>>>>>>>>>>>>>> it. The box is three times the width of the graphene lattice, >>>>>>>>>>>>>>>> three >>>>>>>>>>>>>>>> times the length of the graphene lattice, and three times the >>>>>>>>>>>>>>>> height >>>>>>>>>>>>>>>> between the graphene lattice and the ammonia molecules. I am >>>>>>>>>>>>>>>> including >>>>>>>>>>>>>>>> the mdp file and the error message. >>>>>>>>>>>>>>> Probably your system is exploding when integration fails with >>>>>>>>>>>>>>> excessive >>>>>>>>>>>>>>> forces. You should look at the bottom of stdout, stderr, *and* >>>>>>>>>>>>>>> the .log >>>>>>>>>>>>>>> file to diagnose. The error message you give below is merely the >>>>>>>>>>>>>>> diagnostic trace from the MPI library, and it not useful for >>>>>>>>>>>>>>> finding out >>>>>>>>>>>>>>> what GROMACS thinks the problem might be. Further advice below. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> *************************************************************************** >>>>>>>>>>>>>>>> .mdp file >>>>>>>>>>>>>>>> title =FWS >>>>>>>>>>>>>>>> ;warnings =10 >>>>>>>>>>>>>>>> cpp =cpp >>>>>>>>>>>>>>>> ;define =-DPOSRES >>>>>>>>>>>>>>>> ;constraints =all-bonds >>>>>>>>>>>>>>>> integrator =md >>>>>>>>>>>>>>>> dt =0.002 ; ps >>>>>>>>>>>>>>>> nsteps =100000 >>>>>>>>>>>>>>>> nstcomm =1000 >>>>>>>>>>>>>>>> nstxout =1000 >>>>>>>>>>>>>>>> ;nstvout =1000 >>>>>>>>>>>>>>>> nstfout =0 >>>>>>>>>>>>>>>> nstlog =1000 >>>>>>>>>>>>>>>> nstenergy =1000 >>>>>>>>>>>>>>>> nstlist =1000 >>>>>>>>>>>>>>>> ns_type =grid >>>>>>>>>>>>>>>> rlist =2.0 >>>>>>>>>>>>>>>> coulombtype =PME >>>>>>>>>>>>>>>> rcoulomb =2.0 >>>>>>>>>>>>>>>> vdwtype =cut-off >>>>>>>>>>>>>>>> rvdw =5.0 >>>>>>>>>>>>>>>> fourierspacing =0.12 >>>>>>>>>>>>>>>> fourier_nx =0 >>>>>>>>>>>>>>>> fourier_ny =0 >>>>>>>>>>>>>>>> fourier_nz =0 >>>>>>>>>>>>>>>> pme_order =4 >>>>>>>>>>>>>>>> ewald_rtol =1e-5 >>>>>>>>>>>>>>>> optimize_fft =yes >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ; This section added in to freeze hydrogen atoms at edge of >>>>>>>>>>>>>>>> graphene >>>>>>>>>>>>>>>> lattice to prevent movement of lattice >>>>>>>>>>>>>>>> ;energygrp_excl = Edge Edge Edge Grph Grph Grph >>>>>>>>>>>>>>>> freezegrps = Edge Grph ; Hydrogen atoms in graphene >>>>>>>>>>>>>>>> lattice are >>>>>>>>>>>>>>>> associated with the residue Edge >>>>>>>>>>>>>>> See comments in 7.3.24 of manual. You need the energy group >>>>>>>>>>>>>>> exclusions. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Mark >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> freezedim = Y Y Y Y Y Y; Freeze hydrogen atoms in all >>>>>>>>>>>>>>>> directions >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ;Tcoupl =berendsen >>>>>>>>>>>>>>>> ;tau_t =0.1 0.1 >>>>>>>>>>>>>>>> ;tc-grps =protein non-protein >>>>>>>>>>>>>>>> ;ref_t = 300 300 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ;Pcoupl = parrinello-rahman >>>>>>>>>>>>>>>> ;tau_p = 0.5 >>>>>>>>>>>>>>>> ;compressibility = 4.5e-5 >>>>>>>>>>>>>>>> ;ref_p = 1.0 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ;gen_vel = yes >>>>>>>>>>>>>>>> ;gen_temp = 300.0 >>>>>>>>>>>>>>>> ;gen_seed = 173529 >>>>>>>>>>>>>>>> *************************************************************************** >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> *************************************************************************** >>>>>>>>>>>>>>>> ERROR IN OUTPUT FILE >>>>>>>>>>>>>>>> [node16:25758] *** Process received signal *** >>>>>>>>>>>>>>>> [node16:25758] Signal: Segmentation fault (11) >>>>>>>>>>>>>>>> [node16:25758] Signal code: Address not mapped (1) >>>>>>>>>>>>>>>> [node16:25758] Failing at address: 0xfffffffe1233e230 >>>>>>>>>>>>>>>> [node16:25758] [ 0] /lib64/libpthread.so.0 [0x3834a0de80] >>>>>>>>>>>>>>>> [node16:25758] [ 1] >>>>>>>>>>>>>>>> /usr/lib64/libmd_mpi.so.4(pme_calc_pidx+0xd6) >>>>>>>>>>>>>>>> [0x2ba295dd0606] >>>>>>>>>>>>>>>> [node16:25758] [ 2] /usr/lib64/libmd_mpi.so.4(do_pme+0x808) >>>>>>>>>>>>>>>> [0x2ba295dd4058] >>>>>>>>>>>>>>>> [node16:25758] [ 3] /usr/lib64/libmd_mpi.so.4(force+0x8de) >>>>>>>>>>>>>>>> [0x2ba295dba5be] >>>>>>>>>>>>>>>> [node16:25758] [ 4] /usr/lib64/libmd_mpi.so.4(do_force+0x5ef) >>>>>>>>>>>>>>>> [0x2ba295ddeaff] >>>>>>>>>>>>>>>> [node16:25758] [ 5] mdrun_mpi(do_md+0xe23) [0x411193] >>>>>>>>>>>>>>>> [node16:25758] [ 6] mdrun_mpi(mdrunner+0xd40) [0x4142f0] >>>>>>>>>>>>>>>> [node16:25758] [ 7] mdrun_mpi(main+0x239) [0x4146f9] >>>>>>>>>>>>>>>> [node16:25758] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) >>>>>>>>>>>>>>>> [0x3833e1d8b4] >>>>>>>>>>>>>>>> [node16:25758] [ 9] mdrun_mpi [0x40429a] >>>>>>>>>>>>>>>> [node16:25758] *** End of error message *** >>>>>>>>>>>>>>>> mpirun noticed that job rank 7 with PID 25758 on node node16 >>>>>>>>>>>>>>>> exited on >>>>>>>>>>>>>>>> signal 11 (Segmentation fault). >>>>>>>>>>>>>>>> 7 processes killed (possibly by Open MPI) >>>>>>>>>>>>>>>> *************************************************************************** >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Could you please let me know what you think may be causing the >>>>>>>>>>>>>>>> fault? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Much thanks in advance. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Darrell Koskinen >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> gmx-users mailing list gmx-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 >>>>>>>>>>> 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 list gmx-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 mailing list >>>>>>>>> gmx-users@gromacs.org >>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>>>>>> Please search the archive at http://www.gromacs.org/search before >>>>>>>>> posting! >>>>>>>>> >>>>>>>>> End of gmx-users Digest, Vol 63, Issue 61 >>>>>>>>> ***************************************** >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> gmx-users mailing list gmx-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 mailing list gmx-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 >>>>> 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 list >>>>> gmx-users@gromacs.org >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at http://www.gromacs.org/search before posting! >>>>> >>>>> End of gmx-users Digest, Vol 63, Issue 74 >>>>> ***************************************** >>>>> >>>> _______________________________________________ >>>> gmx-users mailing list gmx-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 >>> 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 list >>> gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before posting! >>> >>> End of gmx-users Digest, Vol 63, Issue 79 >>> ***************************************** >>> >> _______________________________________________ >> gmx-users mailing list gmx-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 >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 list >gmx-users@gromacs.org >http://lists.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/search before posting! > >End of gmx-users Digest, Vol 63, Issue 85 >***************************************** > _______________________________________________ gmx-users mailing list gmx-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? 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