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The bug was fixed in development version of Charm++. The only visible symptom is that the number of unique compute nodes reported at startup is one larger than the correct value (run on 20 nodes, NAMD reports 21). Lone pairs used in Drude force field may be positioned incorrectly (at wrong angles) if the patch grid has only one patch in some dimension (e.g., 3 x 1 x 2) I do not understand how this >>> could have happened since I imaged my water molecules in CHARMM by residue. >>> Can someone please tell me if there is a quick

I would assume that when heated, the system might initially contract, but then would expand to the gas phase as the heating continues. FATAL ERROR: child atom x bonded only to child H atoms One cause of this error (other than having a bad input structure) is that NAMD can incorrectly assume, internally, that gdb namd2 core ... On my Windows version of VMD the bonds to the hydrogen > atoms of my water molecules look elongated, but on the UNIX version it does > not.

Since the problem, I tried to use the input coordinates of the > file that I used to run NPT dynamics in CHARMM and this also did not work. > The Remember to subtract 1 from NAMD's atom ID to get VMD's atom index (or use SERIAL in VMD instead of index). Unlike exclusion count errors, however, they will not occur in serial simulations, and may remain hidden until a large enough parallel run is attempted If extraBonds is being used to add FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html And then the job crashes completely.

To be efficient use a binary search, for example: crashes on entire cluster (nodes 0-31) runs on nodes 0-15, crashes on nodes 16-31 runs on nodes 0-15,16-23, crashes on nodes 0-15,24-31 This extra memory is distributed across processors during a parallel run, but a single workstation may run out of physical memory with a large system. Can anyone suggest how I can find the source of this error? It is possible to cause instability in an interactive (IMD) simulation by attempting to steer the simulation too enthusiastically.

As an alternative, the SMP builds share molecular data within a node, allowing larger simulations to run on a given machine. For 1-4 modified exclusions, only excluded pairs within the cutoff distance are counted. For example, setting switchdist equal to cutoff will cause these errors. (If you don't want switching, just say switching off and all is well.) These can also be generated if your Check with the "top" command.

Below I copy the configuration file and the colvars input file. > >> > >> Regards, > >> > >> Maria > >> > >> Config. student of Bio-nanotechnology > Next message: Cesar Luis Avila: "Turning off tcl forces" Previous message: Huy N. Did you minimize to eliminate bad contacts before starting dynamics? Workaround is to add fake parameters for reported atom type combinations to parameter file.

Peter Huy N. The situation is analogous for bond, angle, dihedral, >> or improper count errors. >> >> This is often caused by similar input problems as in "Atoms moving too >> fast" above. If this happens right away in the simulation: Is your periodic cell large enough for your system? You have too small a cutoff when minimizing. 3.

Duplicate atoms can be found with the following script: $ while read i; do grep -e "$i" surf01_03.pdb; done < <( grep ATOM surf01_03.pdb | awk '{coord=substr($0,31,24);print coord}') > surf01_03.tmp If Workaround is to use twoawayx, twoawayy, or twoawayz to force patch splitting in narrow dimensions. Repeatable core dumps NAMD should exit gracefully, but sometimes we miss something. You might need to > use 'regenerate angles dihedrals' immediately after the patch, in your > configuration file.

All excluded pairs of atoms should be well within the cutoff distance and net system motion shouldn't matter. > 2). Warning: Bad global improper count! Ha: "RE: FATAL ERROR: Bad global exclusion count" Reply: Huy N. FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html Stack Traceback: [0] _ZN10Controller9algorithmEv+0x4e8 [0x81f46a8] [1] _ZN10Controller9threadRunEPS_+0xc [0x8200a06] [2] /usr/local/namd/namd2.i686 [0x82eddb5] [3] Charm++ Runtime: Converse thread (qt_args+0x72 [0x83722ee]) Fatal error on PE 0> FATAL ERROR: Bad global

Try looking at your input psf and pdb files in VMD. If that works then the problem is likely contention at the DNS server. This is often caused by similar input problems as in "Atoms moving too fast" above. PATCH NTER P1:1 ...

Random core dumps This is probably NAMD's fault, and there's not much you can do, unless it's really due to: bad compiler bad memory bad PCI bus bad network hardware bad For more information on instantaneous forces, you could enable the outputAppliedforce option in the colvar. I increased the pairlist distance and set "COMmotion no" after the > first instance, but still encountered the same error around ~20-23 ns. > Temperature, potential and kinetic energies are all Another workaround is to download the latest Charm++ from http://charm.cs.uiuc.edu.

Thank you, Jim Next message: Andrea Diaz: "TEMPERATURE and TEMPAVG : nan" Previous message: Ilya Chorny: "Re: Pairinteractions" Messages sorted by: [ date ] [ thread ] [ subject ] [ If you restart from the last checkpoint before the error does it run for another 20ns? If your cell is smaller than this and you get these warnings then NAMD is possibly ignoring nonbonded interactions between different images of the same molecule, which is not correct. If this happens when continuing a simulation: If you're running constant pressure did you remember to use the extendedSystem parameter to load the .xsc file that corresponds to your restart coordinates?

since these daemons start the shells that start the namd2 binary. Yongye: "Low global exclusion count errors" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] This archive was generated by hypermail 2.1.6 See if that helps. > > Mr. If it is not finding a library that exists, try putting it in your LD_LIBRARY_PATH.

These will typically have abnormally long bonds and they will probably move several Angstroms at the start of minimization. Using psfgen I read them in separately and created separate segments for them. I reset the margin to 0 and I am still > getting the same issue. Yongye wrote: > Dear NAMD users, I ran into the "Low global exclusion count errors" > after about 20 ns of production dynamics. > > 1).

If you experience hangs at startup while determining CPU topology, try adding +skip_cpu_topology to the command line. MStream checksum errors Something is very wrong with your network or your NAMD binary.