Re: equilibrate the bulk water system

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Fri Mar 13 2015 - 11:28:35 CDT

Hasan,

The problem is with your parameter file:

1. Bond: OS HS 0.0 1.0
Which means: spring constant 0.0, distance 1.0

2. Angle: HS OS HS 0.0 109.47
Which means: spring constant 0.0, angle 109.47

3. You don't use rigid bonds (i.e., in config file you don't specify: rigidBonds water)

During minimization bonds in water molecules collapse, angles become 180, and you get this error message in the end. So, you get exactly what you ask for given the parameter file you feed in.

Try using a spring constant of 450 for OH bond, a spring constant of 55.00 for HOH angle.

OS HS 450.0 1.0
HS OS HS 55.0 109.47

Another, minor note: edit your parameter file in a different text editor...

Maxim

> On Mar 13, 2015, at 6:57 AM, Hasan haska <hasanhaska_at_REMOVE_yahoo.com> wrote:
>
> 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 150000
> reinitvels $temperature
> run 10000000
> # 10 ns 2002 record
>
>
> On Wednesday, March 11, 2015 5:19 PM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
>
>
> From the Error message one can conclude instability of your system. The error message points out, that the grid charges for PME have changed more than expected between timesteps, which results from really fast atoms. The most likely reason are bad contacts in the initial structure and too short minimization. So increase the number of minimization steps to approx. 10000 steps. Also check the TOTAL energy of the system for convergence during the minimization run (VMDs Namd Plot plugin is useful for that).  <applewebdata://08DD3952-CCA9-4024-A3C1-8BBA4D117F5F>
>
> 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 that includes 7048 water molecules (SPC/E water model) in a rectangular box with the d=0.996 g/cm3 experimental density at 300K. Therefore I prepared a namd conf file below and started to run it. But after minimization was completed I got the error, which is in below. My aim is to run minimization and NPT simulation with keeping the dimension of the unit cell in the x-y plane constant while allowing fluctuations along the z axis in order to get the real cell sizes ( 55 X 55 X 70 Angs ) according to the density. Then run a NVT simulation with these cell size. How can I solve this problem ? Could you please share your opinion and experience ?
>
>
> Thanks.
>
>
> http://www.filedropper.com/water_1 <http://www.filedropper.com/water_1>
>
> My simulation files are in the link above.
>
>
> *****************************
> Error:
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Stray PME grid charges detected!
>
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
>
> Charm++ fatal error:
> FATAL ERROR: 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 #
>
> 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 10000
> reinitvels $temperature
> run 10000000
> # 10 ns 2002 record

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