AMBER Archive (2008)
Subject: Re: AMBER: increasing temperature smoothly

From: Germain Vallverdu (germain.vallverdu_at_lcp.u-psud.fr)
Date: Mon Sep 22 2008 - 06:31:56 CDT

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Thank you for your previous help, my input now work correctly, but I am
still not sure of what it will do.
This is my input

***********************************************************************
equilibration a volume constant thermalisation avec contrainte prot
&cntrl
nstlim=50000, dt=0.002,
irest=0, ntx=1, t=0.0, ig=190908,
ntpr=1000, ntwr=1000, ntwx=1000, iwrap=1,
tempi=100.0, temp0=300.0, ntt=3, gamma_ln=1.0,
ntb=1, ntp=0,
ntc=2, ntf=2,
cut=10.0
ntr=1, restraint_wt=5.0, restraintmask=":1-227",
nmropt=1,
/
&wt
type='TEMP0',
istep1=1,
istep2=20000,
istep2=0,
imult=0,
iinc=0,
value1=100,
value2=300,
/
&wt
type='END'
/
****************************************

And I got that on the output :

Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
TEMP0 1 0 100.000000 300.000000 0 0
Warning: ISTEP1 >= ISTEP2

RESTRAINTS:
** No restraint defined **

Done reading weight changes/NMR restraints

It looks like sander does not correctly read the istep1 and istep2 or I
do not understand the warning. I put a the end of this mail the mdout file, I think TEMP0 is
always 100K and do not smoothly increase after 20000 steps TEMP is still
around 100K.

An other thing, I change my input in order to use new flags for
restraint with ntr=1 (restraint_wt and restraintmask). I got the correct
number of atoms but the restraint_wt value never appears in the output
file (only at the beginning in my input), is it ok and is it a way to
check that the value is correctly read ?

Thanks

Germain

mdout :

          -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------

| Run on 09/22/2008 at 05:59:33
[-O]verwriting output

|INPTRA: inptraj
|

Here is the input file:

equilibration a volume constant thermalisation avec contrainte prot
&cntrl
nstlim=50000, dt=0.002,
irest=0, ntx=1, t=0.0, ig=190908,
ntpr=1000, ntwr=1000, ntwx=1000, iwrap=1,
tempi=100.0, temp0=300.0, ntt=3, gamma_ln=1.0,
ntb=1, ntp=0,
ntc=2, ntf=2,
cut=10.0
ntr=1, restraint_wt=5.0, restraintmask=":1-227",
nmropt=1,
/
&wt
type='TEMP0',
istep1=1,
istep2=20000,
istep2=0,
imult=0,
iinc=0,
value1=100,
value2=300,
/
&wt
type='END'
/

--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags: MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read

| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 27.854
| New format PARM file being parsed.
| Version = 1.000 Date = 07/24/08 Time = 18:04:28
NATOM = 27219 NTYPES = 17 NBONH = 25405 MBONA = 1851
NTHETH = 4047 MTHETA = 2506 NPHIH = 7734 MPHIA = 4855
NHPARM = 0 NPARM = 0 NNB = 51324 NRES = 8110
NBONA = 1851 NTHETA = 2506 NPHIA = 4855 NUMBND = 58
NUMANG = 123 NPTRA = 44 NATYP = 38 NPHB = 1
IFBOX = 1 NMXRS = 40 IFCAP = 0 NEXTRA = 0
NCOPY = 0

BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

General flags:
imin = 0, nmropt = 1

Nature and format of input:
ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 1000, ntrx = 1, ntwr = 1000
     iwrap = 1, ntwx = 1000, ntwv = 0, ntwe = 0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0

Potential function:
     ntf = 2, ntb = 1, igb = 0, nsnb = 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
ibelly = 0, ntr = 1

Molecular dynamics:
nstlim = 50000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000

Langevin dynamics temperature regulation:
ig = 190908
temp0 = 300.00000, tempi = 100.00000, gamma_ln= 1.00000

SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001

NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 55.707 Box Y = 67.721 Box Z = 71.744
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 60 NFFT2 = 72 NFFT3 = 72
     Cutoff= 10.000 Tol =0.100E-04
     Ewald Coefficient = 0.27511
     Interpolation order = 4

LOADING THE CONSTRAINED ATOMS AS GROUPS

5. REFERENCE ATOM COORDINATES

Mask :1-227; matches 3580 atoms

--------------------------------------------------------------------------------
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 0 100.000000 300.000000 0 0
Warning: ISTEP1 >= ISTEP2

RESTRAINTS:
** No restraint defined **

Done reading weight changes/NMR restraints

Number of triangulated 3-point waters found: 7878
| Atom division among processors:
| 0 3414 6804 10206 13608 17010 20412 23814
| 27219

Sum of charges from parm topology file = -0.00000010
Forcing neutrality...
| Running AMBER/MPI version on 8 nodes

--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------

---------------------------------------------------
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 = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8350E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 1285982
| TOTAL SIZE OF NONBOND LIST = 9860526

NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 144.71 PRESS = 0.0
Etot = -110687.6567 EKtot = 8088.1491 EPtot = -118775.8058
BOND = 118.2113 ANGLE = 543.0451 DIHED = 1870.1948
1-4 NB = 708.8992 1-4 EEL = 10994.4530 VDWAALS = 16431.8065
EELEC = -149442.4157 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.4026E-04
------------------------------------------------------------------------------