Re: equilibrate the bulk water system

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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