Re: Re: Simulation in water sphere meet with a FATAL ERROR about Bad global exclusion count

From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Sun Nov 04 2007 - 22:05:29 CST

Hi, too sorry to send the third email to disturb you.

When the 89 residue is deleted, the 88 residue Glu becomes the last residue,
when I use autopsf to generate the psf and use CTER patch, I find that, the
88 Glu has 4 O atom, OT1, OT2, OE1 OE2. Should I not use the CTER patch or
delete either OT1 or OT2.

Too sorry to send you three email at one time. I am indeed very anxious
about it.

After CTER patch, this is the atom coordinates of last residue Glu 88:

ATOM 1345 C GLU A 88 18.388 -5.329 2.808 1.00 0.00 P1
C
ATOM 1346 OT1 GLU A 88 18.435 -4.333 2.887 0.00 0.00 P1
O
ATOM 1347 OT2 GLU A 88 18.687 -6.170 3.258 0.00 0.00 P1
O
ATOM 1348 N GLU A 88 17.112 -4.455 0.869 1.00 0.00 P1
N
ATOM 1349 HN GLU A 88 17.679 -4.190 0.094 0.00 0.00 P1
H
ATOM 1350 CA GLU A 88 17.573 -5.692 1.563 1.00 0.00 P1
C
ATOM 1351 HA GLU A 88 16.731 -6.312 1.829 1.00 0.00 P1
H
ATOM 1352 CB GLU A 88 18.451 -6.415 0.541 1.00 0.00 P1
C
ATOM 1353 HB1 GLU A 88 18.972 -7.135 1.000 0.00 0.00 P1
H
ATOM 1354 HB2 GLU A 88 19.131 -5.707 0.089 1.00 0.00 P1
H
ATOM 1355 CG GLU A 88 17.571 -7.040 -0.542 1.00 0.00 P1
C
ATOM 1356 HG1 GLU A 88 17.136 -6.316 -1.077 0.00 0.00 P1
H
ATOM 1357 HG2 GLU A 88 16.810 -7.653 -0.078 1.00 0.00 P1
H
ATOM 1358 CD GLU A 88 18.432 -7.907 -1.463 1.00 0.00 P1
C
ATOM 1359 OE1 GLU A 88 19.030 -7.356 -2.372 1.00 0.00 P1
O
ATOM 1360 OE2 GLU A 88 18.480 -9.106 -1.242 1.00 0.00 P1
O

On 11/4/07, Shulin Zhuang <shulin.zhuang_at_gmail.com> wrote:
>
> Sorry to add some information, I use 6 Na+ to neutralize the protein
> -water system, however, after minimizing the system, these 6 Na+ seems
> forming bonds with the TIP3P water. I do not know how to tackle this
> problem. Shoud I delete the water involving with Na+. before the MD
>
> On 11/4/07, Shulin Zhuang <shulin.zhuang_at_gmail.com> wrote:
> >
> > Dear All,
> >
> > I do equilibration MD simulation of protein in water sphere with NAMD2.6.
> > The protein is I27, 89 resiudes,pdb 1tit. I have once sucessfully do 1 ns
> > equilibration of I 27. However, when this time, I just delete the last
> > residue 89, when I run equilibration at 392 ns, the MD stops and give the
> > error information:FATAL ERROR: Bad global exclusion count! How can I tackle
> > this problem.
> >
> > Here, I put my configuration file of equilibration MD. Wish anyone will
> > help me out of this problem. Great thanks. Following is the configuration
> > file. For this configuration file, I just use it to do 1 ns equlibration of
> > I 27 without deleting residue 89.
> >
> >
> > #############################################################
> > ## Production run MD run ##
> > ## in Water Sphere ##
> > #############################################################
> >
> > #############################################################
> > ## ADJUSTABLE PARAMETERS ##
> > #############################################################
> >
> > # molecular system
> > set MOL 1tit
> > structure ${MOL}_sol_ionize.psf
> >
> > set outputname ${MOL}_prod
> > set prod_restart ${MOL}_prod_restart
> >
> > # after heating system
> > set inprot ${MOL}_heat
> > coordinates ${inprot}.coor
> > velocities ${inprot}.vel
> > extendedSystem ${inprot}.xsc
> >
> > set temperature 300 ;# initial temperature
> >
> > # Continuing a job from the restart files
> > if {0} {
> > set inputname myinput
> > binCoordinates $inputname.restart.coor
> > binVelocities $inputname.restart.vel ;# remove the "temperature"
> > entry if you use this!
> > extendedSystem $inputname.xsc
> > }
> >
> > firsttimestep 0
> >
> > #############################################################
> > ## SIMULATION PARAMETERS ##
> > #############################################################
> >
> > # Input
> > paraTypeCharmm on
> > parameters par_all27_prot_lipid_na.inp
> >
> > # Spherical boundary conditions
> > sphericalBC on
> > sphericalBCcenter -1.9094337225 0.573376715183 0.0411463677883
> > sphericalBCr1 31.2752613824
> > sphericalBCk1 10
> > sphericalBCexp1 2
> >
> > # Force-Field Parameters
> > exclude scaled1-4
> > 1-4scaling 1.0
> > cutoff 13.0
> > switching on
> > switchdist 10.0
> > pairlistdist 14.5
> >
> >
> > # Integrator Parameters
> > timestep 1.0 ;# 1fs/step
> > nonbondedFreq 2
> > fullElectFrequency 4
> > stepspercycle 20
> >
> > # Constant Temperature Control
> > # A: for heating, use temperature reassignment
> > if {0} {
> > reassignFreq 500 ;# tuned to be suit 'natural' heating for system.
> > reassignTemp 25 ;# to start from 0 Kelvin, else always lagging by
> > 25K.
> > reassignIncr 25
> > reassignHold $temperature
> > }
> >
> > # B: for heating, Temperature coupling via Langevin dynamics
> > if {1} {
> > langevin on ;# do langevin dynamics
> > langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> > langevinTemp $temperature
> > langevinHydrogen no ;# couple langevin bath to hydrogens
> > }
> >
> > # Constant Pressure Control (variable volume)
> > if {0} {
> > useGroupPressure yes ;# needed for 2fs steps
> > useFlexibleCell no ;# no for water box, yes for membrane
> > useConstantArea no ;# no for water box, yes for membrane
> > langevinPiston on
> > langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> > langevinPistonPeriod 100
> > langevinPistonDecay 50
> > langevinPistonTemp $temperature
> > }
> >
> > # for saving restart file
> > if {0} {
> > restartname $prod_restart
> > restartfreq 200 ;# 500steps = every 0.5ps
> > restartsave yes
> > binaryrestart yes ;# yes will preserves more accuracy.
> > }
> >
> > # Output
> > outputName $outputname
> > dcdfreq 200
> > xstFreq 200
> > outputEnergies 100
> > outputTiming 100
> > binaryoutput yes
> >
> > # Fixed Atoms Constraint (set PDB beta-column to 1)
> > if {0} {
> > fixedAtoms on
> > fixedAtomsForces on
> > fixedAtomsFile fix_backbone.pdb
> > fixedAtomsCol B
> > }
> >
> > # IMD Settings (can view sim in VMD)
> > if {0} {
> > IMDon on
> > IMDport 3000 ;# port number (enter it in VMD)
> > IMDfreq 1 ;# send every 1 frame
> > IMDwait no ;# wait for VMD to connect before running?
> > }
> >
> > #############################################################
> > ## EXTRA PARAMETERS ##
> > #############################################################
> >
> > # Put here any custom parameters that are specific to
> > # this job (e.g., SMD, TclForces, etc...)
> >
> > #constantforce yes
> > #consforcefile ../common/example-output/ubq_ww_eq2.ref
> >
> > #############################################################
> > ## EXECUTION SCRIPT ##
> > #############################################################
> >
> > # Minimization
> > if {0} {
> > minimize 3000
> > }
> >
> > run 1000000
> > #production for 1ns
> >
> >
> >
> >
> >
>

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