**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Sun Mar 15 2015 - 21:30:06 CDT

**Next message:**Payel Das: "Postdoc positions available at IBM (bio-molecular modeling and MD)"**Previous message:**Hasan haska: "Re: equilibrate the bulk water system"**In reply to:**Hasan haska: "Re: equilibrate the bulk water system"**Next in thread:**Abhishek Tyagi: "Re: equilibrate the bulk water system"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

On Mar 15, 2015 9:45 PM, "Hasan haska" <hasanhaska_at_remove_yahoo.com> wrote:

*>
*

*> Dear Maxim Belkin,
*

*>
*

*> Thank you for your valuable explanation. I used a spring constant of 450
*

for OH bond and a spring constant of 55.00 for HOH angle in my parameter

file as you advised. And the problem was solved. But should I also use

“rigidBonds water” or “rigidBonds all” definition in conf file ?

SPC/E is a rigid water model.

*>
*

*> My definitions for hydrogen and oxygen molecules are 0S1, HS2, HS3 and
*

types are OS and HS ? I think that these are not the same in general charmm

prm file. Can ıt be known by namd that I use water molecules in my

simulation system ?

Make sure you don't confuse atom names with atom types.

*>
*

*> And I also found another namd prm file for SPC/E water model which is in
*

below. And I realized that this prm file is different form my prm file.

Could you please help me about choosing the suitable SPC/E prm values for

my bulk water simulation ?

The parameter sets are equivalent for as long as you use rigid bonds/angles

for the water molecules. In that case only the value for the equilibrium

distance / angle is required.

Axel

*>
*

*> *****************
*

*> My prm File: SPC/E
*

*>
*

*> BONDS
*

*>
*

*> !V(bond) = Kb(b - b0)**2
*

*> !Kb: kcal/mole/A**2
*

*> !b0: A
*

*> !atom type Kb b0
*

*>
*

*> OS HS 450.0 1.000
*

*>
*

*>
*

*> ANGLES
*

*>
*

*> !V(angle) = Ktheta(Theta - Theta0)**2
*

*> !V(Urey-Bradley) = Kub(S - S0)**2
*

*> !Ktheta: kcal/mole/rad**2
*

*> !Theta0: degrees
*

*> !Kub: kcal/mole/A**2 (Urey-Bradley)
*

*> !S0: A
*

*> !atom types Ktheta Theta0 Kub S0
*

*>
*

*>
*

*> HS OS HS 55.0 109.47
*

*>
*

*>
*

*> NONBONDED
*

*>
*

*> !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
*

*> !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
*

*> !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
*

*> !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
*

*>
*

*>
*

*> OS 0. -0.1553943 1.7766 0. -0.1553943 1.7766
*

*> HS 0. 0.0000 0.0 0. 0.0000 0.0
*

*>
*

*> END
*

*> *************
*

*>
*

*>
*

*>
*

*>
*

*>
*

*> **************
*

*> Another PRM File : SPC/E
*

*>
*

*> BONDS
*

*>
*

*> !V(bond) = Kb(b - b0)**2
*

*> !Kb: kcal/mole/A**2
*

*> !b0: A
*

*> !atom type Kb b0
*

*>
*

*> OS HS 600.000 1.000
*

*>
*

*>
*

*> ANGLES
*

*>
*

*> !V(angle) = Ktheta(Theta - Theta0)**2
*

*> !V(Urey-Bradley) = Kub(S - S0)**2
*

*> !Ktheta: kcal/mole/rad**2
*

*> !Theta0: degrees
*

*> !Kub: kcal/mole/A**2 (Urey-Bradley)
*

*> !S0: A
*

*> !atom types Ktheta Theta0 Kub S0
*

*>
*

*>
*

*> HS OS HS 124.00 109.50
*

*>
*

*>
*

*> NONBONDED
*

*>
*

*> !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
*

*> !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
*

*> !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
*

*> !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
*

*>
*

*>
*

*> HS 0.000000 -0.000000 0.000000
*

*> OS 0.000000 -0.155298 1.776857
*

*>
*

*>
*

*>
*

*> END
*

*>
*

*> ***********
*

*>
*

*>
*

*>
*

*>
*

*>
*

*> On Friday, March 13, 2015 7:20 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu>
*

wrote:

*>
*

*>
*

*> 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).

*>>
*

*>> 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
*

*>>
*

*>> 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
*

*>
*

*>
*

*>
*

*>
*

**Next message:**Payel Das: "Postdoc positions available at IBM (bio-molecular modeling and MD)"**Previous message:**Hasan haska: "Re: equilibrate the bulk water system"**In reply to:**Hasan haska: "Re: equilibrate the bulk water system"**Next in thread:**Abhishek Tyagi: "Re: equilibrate the bulk water system"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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