From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Fri Jul 24 2015 - 13:38:52 CDT
What is happening with your box dimensions (in the XSC file)? If you
print on a relatively small interval, to you see them decreasing, or
remaining constant? What does your simulation look like when you
visualize a pre-patch grid error set of coordinates in VMD? My gut
feeling is that you probably don't have enough water in the system to
get to a stable equilibrium density, and are likely forming "bubbles" as
the water condenses. Your water density is low. It should be closer to
0.99 g/cm^3, not 0.89 g/cm^3.
-- ---- Jeffrey Potoff Professor & Director of Early Engineering Programs Department of Chemical Engineering and Materials Science Wayne State University http://potoff1.eng.wayne.edu http://gomc.eng.wayne.edu On 07/24/2015 02:14 PM, Merrill, Dante wrote: > > Hello, > > I am well aware of the multitude of patch-size errors on the mailing > list and I have read through the majority of them and have yet to find > a good answer that fits my issue. Please just read the next paragraph > and then judge whether this is like the other issues posted to the > mailing list. > > I am attempting to correctly equilibrate and produce a relatively > small protein (~50,000 atoms) in a water box (currently ~15,000) for a > total of 100 ns using 2 fs timesteps using NPT (config file for > production run 1 below). I have added margin, turned Flexiblecell on > and off (and its two counterparts), restarted, elongated minimization > and equilibration, checked the water density (its at 0.89 g/cm^3), > resolvated, moved the origin to 0,0,0 , and messed with pairlistdist > and switchdist settings. > > I can get through my 10,000 step minimization, and 4 200,000 step > equilibrations just fine. However I cannot for the life of me get my > production run to go past 6 million steps without having to restart. > Which would be annoying but do able if not for the fact that after > every restart my patch size decreases so by restart 4 I am getting > about 200,000 steps per run. > I understand that you receive a lot of emails about this issue and I > am sorry to have to add to that however I feel I have exhausted my > resources in trying to figure this out myself and I humbly ask for > your help with this issue. Any guidance as to how to fix this or even > just elongate my runs would be greatly appreciated. > > > Thank you for your time and efforts. > > > Best, > > Dante > > > > timestep 2.0 > numsteps 50000000 # 100000000fs = 100000ps = 100ns > > useConstantRatio yes > useflexiblecell yes > useConstantArea no > > #structure ../scr/syt1_pops_prot_final.pdb.xplor.psf > structure ../scr/final2_slp4.psf > paraTypeCharmm on > > > # INPUT > #coordinates ../scr/syt1_pops_prot_final.pdb.solv.pdb > #bincoordinates ../scr/equilibration/equil5.coor > #binvelocities ./scr/equilibration/equil5.vel > coordinates ../scr/equilibration/equil4.coor > velocities ../scr/equilibration/equil4.vel > extendedsystem ../scr/equilibration/equil4.xsc > > # OUTPUT > outputenergies 1000 > outputtiming 1000 > outputpressure 1000 > binaryoutput no > > outputname ../scr/production/prod1 > restartname ../scr/production/prod1 > restartfreq 10000 > binaryrestart yes > > XSTFreq 1000 > > dcdfile ../dcd/prod1.dcd > dcdfreq 1000 > > # CUT-OFFs > vdwForceSwitching on > splitpatch hydrogen > hgroupcutoff 3.0 > stepspercycle 10 > switching on > switchdist 11.0 > cutoff 12.0 > pairlistdist 20.0 > pairlistsPerCycle 2 > # H-MATRIX > > # CONSTANT-T > langevin on > #langevintemp 310.0 > langevintemp 298.0 > langevindamping 1.0 > > # CONSTANT-P > langevinpiston on > > > langevinpistontarget 1 > langevinpistonperiod 200 > langevinpistondecay 50 > #langevinpistontemp 310 > langevinpistontemp 298 > > strainrate 0. 0. 0. > usegrouppressure yes > > # PME > PME yes > PMETolerance 10e-5 > PMEInterpOrder 4 > PMEGridSpacing 1.0 > > # MULTIPLE TIME-STEP > fullelectfrequency 2 > nonbondedfreq 1 > > # SHAKE/RATTLE > rigidbonds all > rigidtolerance 0.00001 > rigiditerations 400 > > # 1-4's > exclude scaled1-4 > 1-4scaling 1.0 > > > #parameters ../lib/par_all36_na.prm > #parameters ../lib/par_all36_lipid.prm > parameters ../lib/par_all36_prot.prm > parameters ../lib/toppar_water_ions.str > > >
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