From: Hasan haska (hasanhaska_at_yahoo.com)
Date: Fri Mar 13 2015 - 06:57:15 CDT
Dear Norman Geist,
I increased the min. step form 100000 to 150000 as you adviced and run the conf file in below again. But I got the same error "Reason: FATAL ERROR: Stray PME grid charges detected!" . What should I do to solve this error ? Could you please suggest a right procedure to equilibriate the bulk water simulation system ?
Thaks in advance.
#--- This is a test namd configuration file
#############################################################
##
#############################################################
paratypeCharmm on
parameters water.PRM
structure water.psf #
coordinates water_.pdb #
outputName water_1out #
set temperature 300
temperature $temperature
firsttimestep 0
# Integrator Parameters
timestep 1.0
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 16
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 18.
switching on
switchdist 15.
pairlistdist 20.
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen on ;# couple langevin bath to hydrogens
# Constant Pressure Control (variable volume)
useGroupPressure no ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea yes ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 50.
langevinPistonTemp $temperature
#--- PBC
cellBasisVector1 55.0 0.0 0.0
cellBasisVector2 0.0 55.0 0.0
cellBasisVector3 0.0 0.0 100.0
#--- PME
PME yes
PMEGridSpacing 1.0
#--- Output & Restart
binaryoutput no
binaryrestart yes
restartname water_1restart #
DCDfile water_1out.dcd #
restartfreq 5000 #
dcdfreq 5000
xstFreq 5000
outputEnergies 5000
outputPressure 5000
outputtiming 5000
minimize 150000reinitvels $temperature
run 10000000
# 10 ns 2002 record
On Wednesday, March 11, 2015 5:19 PM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
#yiv9125586955 #yiv9125586955 -- _filtered #yiv9125586955 {panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv9125586955 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;} _filtered #yiv9125586955 {font-family:Tahoma;panose-1:2 11 6 4 3 5 4 4 2 4;} _filtered #yiv9125586955 {panose-1:0 0 0 0 0 0 0 0 0 0;}#yiv9125586955 #yiv9125586955 p.yiv9125586955MsoNormal, #yiv9125586955 li.yiv9125586955MsoNormal, #yiv9125586955 div.yiv9125586955MsoNormal {margin:0cm;margin-bottom:.0001pt;font-size:12.0pt;}#yiv9125586955 a:link, #yiv9125586955 span.yiv9125586955MsoHyperlink {color:blue;text-decoration:underline;}#yiv9125586955 a:visited, #yiv9125586955 span.yiv9125586955MsoHyperlinkFollowed {color:purple;text-decoration:underline;}#yiv9125586955 span.yiv9125586955E-MailFormatvorlage18 {color:#1F497D;}#yiv9125586955 .yiv9125586955MsoChpDefault {font-size:10.0pt;} _filtered #yiv9125586955 {margin:70.85pt 70.85pt 2.0cm 70.85pt;}#yiv9125586955 div.yiv9125586955Section1 {}#yiv9125586955 From the Error messageone can conclude instability of your system. The error message points out, thatthe grid charges for PME have changed more than expected between timesteps,which results from really fast atoms. The most likely reason are bad contactsin the initial structure and too short minimization. So increase the number ofminimization steps to approx. 10000 steps. Also check the TOTAL energy of thesystem for convergence during the minimization run (VMDs Namd Plot plugin isuseful for that). For the latter NPT run, you are interested in: useflexiblecell yes useconstantarea yes along with the piston pressure to have only Z changing. Norman Geist. From: owner-namd-l_at_ks.uiuc.edu[mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Hasan haska
Sent: Tuesday, March 10, 2015 10:52 PM
To: NAMD List
Subject: namd-l: equilibrate the bulk water system Dear NAMD users, I want to minimize and equilibrate a bulk water system thatincludes 7048 water molecules (SPC/E water model) in a rectangular box with thed=0.996 g/cm3 experimental density at 300K. Therefore I prepared a namdconf file below and started to run it. But after minimization wascompleted I got the error, which is in below. My aim is to run minimization andNPT simulation with keeping the dimension of the unit cell in the x-y planeconstant while allowing fluctuations along the z axis in order to get the realcell sizes ( 55 X 55 X 70 Angs ) according to the density. Then run a NVTsimulation with these cell size. How can I solve this problem ? Could youplease share your opinion and experience ? Thanks. http://www.filedropper.com/water_1 Mysimulation files are in the link above. ***************************** Error: -------------Processor 0 Exiting: Called CmiAbort ------------ Reason:FATAL ERROR: Stray PME grid charges detected! FATALERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html Charm++fatal error: FATALERROR: Stray PME grid charges detected! ************************** #---This is a test namd configuration file ############################################################# ## ############################################################# paratypeCharmm on parameters water.PRM structure water.psf # coordinates water_.pdb # outputName water_1out # settemperature 300 temperature$temperature firsttimestep 0 #Integrator Parameters timestep 1.0 nonbondedFreq 2 fullElectFrequency 4 stepspercycle 16 #Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 18. switching on switchdist 15. pairlistdist 20. #Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 1 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature langevinHydrogen on ;# couple langevin bath to hydrogens #Constant Pressure Control (variable volume) useGroupPressure no ;# needed for 2fs steps useFlexibleCell yes ;# no for water box, yes for membrane useConstantArea yes ;# no for water box, yes for membrane langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 200. langevinPistonDecay 50. langevinPistonTemp $temperature #---PBC cellBasisVector1 55.0 0.0 0.0 cellBasisVector2 0.0 55.0 0.0 cellBasisVector3 0.0 0.0 100.0 #---PME PME yes PMEGridSpacing 1.0 #---Output & Restart binaryoutput no binaryrestart yes restartname water_1restart # DCDfile water_1out.dcd # restartfreq 5000 # dcdfreq 5000 xstFreq 5000 outputEnergies 5000 outputPressure 5000 outputtiming 5000 minimize10000 reinitvels $temperature run10000000 # 10ns 2002 record
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