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From: Abd Ghani Bin Abd Aziz <GS13161.mutiara.upm.edu.my>

Date: Wed, 28 Jul 2004 21:45:55 +0800

Dear Amber,

sorry..i forgot to type my problem... i already create a new script with

nmropt=1. i also removed the group definition (as your advice-actually i

want to restraint but at mean time i just want to see wether the

temperature can cool down or not). the script that i create, i put it at

the bottom of the email. as u mention about the output file, it seems that

everything is fine... but actually the problem still occured..the

temperature heat up untill 200++K and there at the end of simulation, the

temperature is still maintain (not recool to 10K)..

i paste also the output file for you to look at it..

thank you.

Abd Ghani

# Control section

&cntrl

ntwx = 250, ntpr = 50,

ntt = 1, temp0 = 400.0, tempi = 10.0, tautp = 1.0,

scnb = 2.0, scee = 1.2, dielc = 1, cut = 8.0,

ntb = 2, ntc = 2, ntf = 2,

nstlim = 21000, dt = 0.0010,

ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,

ibelly = 0, ntr = 0,

imin = 0, irest = 0, ntx = 1, nmropt = 1,

&end

&ewald

skinnb = 2.0,

nbflag = 1,

&end

&wt

type = 'TEMP0', istep1 = 1, istep2 = 2000, value1 = 10.0, value2 = 400.0,

&end

&wt

type = 'TEMP0', istep1 = 2001, istep2 = 3000, value1 = 400.0, value2 =

400.0,

&end

&wt

type = 'TEMP0', istep1 = 3001, istep2 = 21000, value1 = 400.0, value2 =

10.0,

&end

&wt

type='END'

&end

&rst

iat = 0,

&end

END

________________________________________________________________________

Here is the input file:

# Control section

&cntrl

ntwx = 250, ntpr = 50,

ntt = 1, temp0 = 400.0, tempi = 10.0, tautp = 1.0,

scnb = 2.0, scee = 1.2, dielc = 1, cut = 8.0,

ntb = 2, ntc = 2, ntf = 2,

nstlim = 21000, dt = 0.0010,

ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,

ibelly = 0, ntr = 0,

imin = 0, irest = 0, ntx = 1, nmropt = 1,

&end

&ewald

skinnb = 2.0,

nbflag = 1,

&end

&wt

type = 'TEMP0', istep1 = 1, istep2 = 2000, value1 = 10.0, value2 = 400.0,

&end

&wt

type = 'TEMP0', istep1 = 2001, istep2 = 3000, value1 = 400.0, value2 =

400.0,

&end

&wt

type = 'TEMP0', istep1 = 3001, istep2 = 21000, value1 = 400.0, value2 =

10.0,

&end

&wt

type='END'

&end

&rst

iat = 0,

&end

END

-------------------------------------------------------------------------

1. RESOURCE USE:

getting box info from bottom of parm

getting new box info from bottom of inpcrd

| peek_ewald_inpcrd: Box info found

EWALD SPECIFIC INPUT:

Largest sphere to fit in unit cell has radius = 32.575

Calculating ew_coeff from dsum_tol,cutoff

Box X = 79.791 Box Y = 79.791 Box Z = 79.791

Alpha = 109.471 Beta = 109.471 Gamma = 109.471

NFFT1 = 80 NFFT2 = 80 NFFT3 = 80

Cutoff= 8.000 Tol =0.100E-04

Ewald Coefficient = 0.34864

Interpolation order = 4

NATOM = 33896 NTYPES = 17 NBONH = 31021 MBONA = 2952

NTHETH = 6594 MTHETA = 4023 NPHIH = 11772 MPHIA = 7184

NHPARM = 0 NPARM = 0 NNB = 69551 NRES = 9744

NBONA = 2952 NTHETA = 4023 NPHIA = 7184 NUMBND = 44

NUMANG = 94 NPTRA = 33 NATYP = 30 NPHB = 1

IFBOX = 2 NMXRS = 24 IFCAP = 0

EWALD MEMORY USE:

| Total heap storage needed = 1245

| Adjacent nonbond minimum mask = 69551

| Max number of pointers = 25

| List build maxmask = 139102

| Maximage = 49591

EWALD LOCMEM POINTER OFFSETS

| Real memory needed by PME = 1245

| Size of EEDTABLE = 20918

| Real memory needed by EEDTABLE = 83672

| Integer memory needed by ADJ = 139102

| Integer memory used by local nonb= 1232919

| Real memory used by local nonb = 555525

| MAX NONBOND PAIRS = 100000000

| Memory Use Allocated Used

| Real 10000000 1963082

| Hollerith 10000000 213122

| Integer 10000000 2119605

| Max Nonbonded Pairs:********

BOX TYPE: TRUNCATED OCTAHEDRON

2. CONTROL DATA FOR THE RUN

TIMLIM= 999999. IREST = 0 IBELLY= 0

IMIN = 0

IPOL = 0

NTX = 1 NTXO = 1

IG = 71277 TEMPI = 10.00 HEAT = 0.000

NTB = 2 BOXX = 79.791

BOXY = 79.791 BOXZ = 79.791

NTT = 1 TEMP0 = 400.000

DTEMP = 0.000 TAUTP = 1.000

VLIMIT= 0.000

NTP = 1 PRES0 = 1.000 COMP = 44.600

TAUP = 0.100 NPSCAL= 0

NTCM = 0 NSCM = 9999999

NSTLIM=21000 NTU = 1

T = 0.000 DT = 0.00100

NTC = 2 TOL = 0.00001 JFASTW = 0

NTF = 2 NSNB = 25

CUT = 8.000 SCNB = 2.000

SCEE = 1.200 DIELC = 1.000

NTPR = 50 NTWR = 50 NTWX = 250

NTWV = 0 NTWE = 0 IOUTFM= 0

NTWPRT= 0 NTWPR0= 0 NTAVE= 0

NTR = 0 NTRX = 1

TAUR = 0.00000 NMROPT= 1 PENCUT= 0.10000

IVCAP = 0 MATCAP= 0 FCAP = 1.500

OTHER DATA:

IFCAP = 0 NATCAP= 0 CUTCAP= 0.000

XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000

VRAND= 0

NATOM = 33896 NRES = 9744

Water definition for fast triangulated model:

Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2

3. ATOMIC COORDINATES AND VELOCITIES

begin time read from input coords = 0.000 ps

Begin reading energy term weight changes/NMR restraints

WEIGHT CHANGES:

TEMP0 1 2000 10.000000 400.000000 0 0

TEMP0 2001 3000 400.000000 400.000000 0 0

TEMP0 3001 21000 400.000000 10.000000 0 0

RESTRAINTS:

No valid redirection requests found

** No restraint defined **

Done reading weight changes/NMR restraints

Number of triangulated 3-point waters found: 9377

Sum of charges from parm topology file = -0.00000023

Forcing neutrality...

---------------------------------------------------

APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION

using 5000.0 points per unit in tabled values

TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff

| CHECK switch(x): max rel err = 0.3242E-14 at 2.436720

| CHECK d/dx switch(x): max rel err = 0.8156E-11 at 2.782960

---------------------------------------------------

Total number of mask terms = 59876

Total number of mask terms = 119752

| Total Ewald setup time = 0.09999990

------------------------------------------------------------------------------

-----------------------------------------------------------------------

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Received on Wed Jul 28 2004 - 14:53:00 PDT

Date: Wed, 28 Jul 2004 21:45:55 +0800

Dear Amber,

sorry..i forgot to type my problem... i already create a new script with

nmropt=1. i also removed the group definition (as your advice-actually i

want to restraint but at mean time i just want to see wether the

temperature can cool down or not). the script that i create, i put it at

the bottom of the email. as u mention about the output file, it seems that

everything is fine... but actually the problem still occured..the

temperature heat up untill 200++K and there at the end of simulation, the

temperature is still maintain (not recool to 10K)..

i paste also the output file for you to look at it..

thank you.

Abd Ghani

# Control section

&cntrl

ntwx = 250, ntpr = 50,

ntt = 1, temp0 = 400.0, tempi = 10.0, tautp = 1.0,

scnb = 2.0, scee = 1.2, dielc = 1, cut = 8.0,

ntb = 2, ntc = 2, ntf = 2,

nstlim = 21000, dt = 0.0010,

ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,

ibelly = 0, ntr = 0,

imin = 0, irest = 0, ntx = 1, nmropt = 1,

&end

&ewald

skinnb = 2.0,

nbflag = 1,

&end

&wt

type = 'TEMP0', istep1 = 1, istep2 = 2000, value1 = 10.0, value2 = 400.0,

&end

&wt

type = 'TEMP0', istep1 = 2001, istep2 = 3000, value1 = 400.0, value2 =

400.0,

&end

&wt

type = 'TEMP0', istep1 = 3001, istep2 = 21000, value1 = 400.0, value2 =

10.0,

&end

&wt

type='END'

&end

&rst

iat = 0,

&end

END

________________________________________________________________________

Here is the input file:

# Control section

&cntrl

ntwx = 250, ntpr = 50,

ntt = 1, temp0 = 400.0, tempi = 10.0, tautp = 1.0,

scnb = 2.0, scee = 1.2, dielc = 1, cut = 8.0,

ntb = 2, ntc = 2, ntf = 2,

nstlim = 21000, dt = 0.0010,

ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,

ibelly = 0, ntr = 0,

imin = 0, irest = 0, ntx = 1, nmropt = 1,

&end

&ewald

skinnb = 2.0,

nbflag = 1,

&end

&wt

type = 'TEMP0', istep1 = 1, istep2 = 2000, value1 = 10.0, value2 = 400.0,

&end

&wt

type = 'TEMP0', istep1 = 2001, istep2 = 3000, value1 = 400.0, value2 =

400.0,

&end

&wt

type = 'TEMP0', istep1 = 3001, istep2 = 21000, value1 = 400.0, value2 =

10.0,

&end

&wt

type='END'

&end

&rst

iat = 0,

&end

END

-------------------------------------------------------------------------

1. RESOURCE USE:

getting box info from bottom of parm

getting new box info from bottom of inpcrd

| peek_ewald_inpcrd: Box info found

EWALD SPECIFIC INPUT:

Largest sphere to fit in unit cell has radius = 32.575

Calculating ew_coeff from dsum_tol,cutoff

Box X = 79.791 Box Y = 79.791 Box Z = 79.791

Alpha = 109.471 Beta = 109.471 Gamma = 109.471

NFFT1 = 80 NFFT2 = 80 NFFT3 = 80

Cutoff= 8.000 Tol =0.100E-04

Ewald Coefficient = 0.34864

Interpolation order = 4

NATOM = 33896 NTYPES = 17 NBONH = 31021 MBONA = 2952

NTHETH = 6594 MTHETA = 4023 NPHIH = 11772 MPHIA = 7184

NHPARM = 0 NPARM = 0 NNB = 69551 NRES = 9744

NBONA = 2952 NTHETA = 4023 NPHIA = 7184 NUMBND = 44

NUMANG = 94 NPTRA = 33 NATYP = 30 NPHB = 1

IFBOX = 2 NMXRS = 24 IFCAP = 0

EWALD MEMORY USE:

| Total heap storage needed = 1245

| Adjacent nonbond minimum mask = 69551

| Max number of pointers = 25

| List build maxmask = 139102

| Maximage = 49591

EWALD LOCMEM POINTER OFFSETS

| Real memory needed by PME = 1245

| Size of EEDTABLE = 20918

| Real memory needed by EEDTABLE = 83672

| Integer memory needed by ADJ = 139102

| Integer memory used by local nonb= 1232919

| Real memory used by local nonb = 555525

| MAX NONBOND PAIRS = 100000000

| Memory Use Allocated Used

| Real 10000000 1963082

| Hollerith 10000000 213122

| Integer 10000000 2119605

| Max Nonbonded Pairs:********

BOX TYPE: TRUNCATED OCTAHEDRON

2. CONTROL DATA FOR THE RUN

TIMLIM= 999999. IREST = 0 IBELLY= 0

IMIN = 0

IPOL = 0

NTX = 1 NTXO = 1

IG = 71277 TEMPI = 10.00 HEAT = 0.000

NTB = 2 BOXX = 79.791

BOXY = 79.791 BOXZ = 79.791

NTT = 1 TEMP0 = 400.000

DTEMP = 0.000 TAUTP = 1.000

VLIMIT= 0.000

NTP = 1 PRES0 = 1.000 COMP = 44.600

TAUP = 0.100 NPSCAL= 0

NTCM = 0 NSCM = 9999999

NSTLIM=21000 NTU = 1

T = 0.000 DT = 0.00100

NTC = 2 TOL = 0.00001 JFASTW = 0

NTF = 2 NSNB = 25

CUT = 8.000 SCNB = 2.000

SCEE = 1.200 DIELC = 1.000

NTPR = 50 NTWR = 50 NTWX = 250

NTWV = 0 NTWE = 0 IOUTFM= 0

NTWPRT= 0 NTWPR0= 0 NTAVE= 0

NTR = 0 NTRX = 1

TAUR = 0.00000 NMROPT= 1 PENCUT= 0.10000

IVCAP = 0 MATCAP= 0 FCAP = 1.500

OTHER DATA:

IFCAP = 0 NATCAP= 0 CUTCAP= 0.000

XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000

VRAND= 0

NATOM = 33896 NRES = 9744

Water definition for fast triangulated model:

Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2

3. ATOMIC COORDINATES AND VELOCITIES

begin time read from input coords = 0.000 ps

Begin reading energy term weight changes/NMR restraints

WEIGHT CHANGES:

TEMP0 1 2000 10.000000 400.000000 0 0

TEMP0 2001 3000 400.000000 400.000000 0 0

TEMP0 3001 21000 400.000000 10.000000 0 0

RESTRAINTS:

No valid redirection requests found

** No restraint defined **

Done reading weight changes/NMR restraints

Number of triangulated 3-point waters found: 9377

Sum of charges from parm topology file = -0.00000023

Forcing neutrality...

---------------------------------------------------

APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION

using 5000.0 points per unit in tabled values

TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff

| CHECK switch(x): max rel err = 0.3242E-14 at 2.436720

| CHECK d/dx switch(x): max rel err = 0.8156E-11 at 2.782960

---------------------------------------------------

Total number of mask terms = 59876

Total number of mask terms = 119752

| Total Ewald setup time = 0.09999990

------------------------------------------------------------------------------

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Wed Jul 28 2004 - 14:53:00 PDT

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