From: Hasan haska (hasanhaska_at_yahoo.com)
Date: Sat Mar 14 2015 - 14:38:03 CDT
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 ?
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 ?
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 ?
*****************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 1.7766HS 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 0.000000OS 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 1.0Which means: spring constant 0.0, distance 1.0
2. Angle: HS OS HS 0.0 109.47Which 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 1.0HS 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 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:
>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 yesuseconstantarea 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
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