From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Wed Aug 14 2013 - 23:50:36 CDT
Hi all,
I've been running simulations of a glycosylated protein for some time now using the (relatively) new CHARMM glycan topologies and parameters. To date, I was using these in combination with the NAMD-supplied top/par-all27-prot-lipid-na files which, while everything seemed fine, always worried me slightly regarding a potential mismatch in forces.
In any case, I decided to upgrade to the final CHARMM-c36 release which includes the glycans as part of the official package. The strange thing is that now, in an otherwise perfectly vanilla explicit solvent simulation, my glycan atoms keep failing the RATTLE algorithm at a 2fs timestep. At 1fs everything seems fine - stable simulation, normal-looking glycan conformation with no strangeness in bond lengths or angles and no extreme movements. Just wondering if anyone has any ideas?
My protein/glycan structure is built against the following three topology files:
top_all22_prot.rtf -- included in the c36 package; the CHARMM documentation seems to recommend using this rather than top_all36_prot.rtf for NAMD, and my simulations crash when I try to use the latter
top_all36_carb.rtf
stream/toppar_all36_glycopeptide.str
The simulations are run using:
par_all22_prot.prm
par_all36_carb.prm
stream/toppar_all36_carb_glycopeptide.str
toppar_water_ions.str
I did use VMD's solvate and ionize plugins to add water and ions, which of course uses the topology file included in the NAMD distribution. I don't think this is likely to be causing the problem, though.
As I said, the simulation seems stable at 1fs timesteps. Of course, this slows me down - but I'm more concerned that there's some error here that I'm not seeing, and don't want to waste a million CPU-hours on a production run without checking first. Does anyone have any ideas?
Thanks,
Tristan
Tristan Croll
Lecturer
Faculty of Health
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443
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