Dear Amber's Users.
I mail you because I have a probleme with the Molecular Dynamic. I
observe an
empty gap in the water box from the very beginning of the run. It fills
by
water molecules during the simulation.
Is it normal, what and why is it ? Is it a bug ?
In particular :
When I use the Tutorial 4.3 : "Exemple 3. A more complicated protein
example",
in the part 4.3.6.2 (at the end), and I exectute the molecular dynamic
named
"md1.in" :
Molecular Dynamics Run - md1.in
&cntrl
IMIN = 0, IREST = 0, NTX = 1, TEMPI = 0.,
SCEE = 1.2, IDIEL = 1, CUT =9.0,
NTT = 1, TEMP0 = 300.0, TAUTP=0.2,
NTP = 2, TAUP = 0.2,
NTB = 2, NTC = 4, NTF = 2, NSNB = 25,
NSTLIM = 500,
NTWE = 100, NTWX = 100, NTPR = 25,
&end
with :
sander -O -i md1.in -o md1.out -c min2.xyz -p prmtop.wat -r md1.xyz
-x md1.crd -e md1.en
It produce md1.out, md1.xyz, md1.crd, md1.en.
Part of md1.out :
2. CONTROL DATA FOR THE RUN
TIMLIM= 999999. IREST = 0 IBELLY= 0
KFORM = 1 ICHDNA= 0 IMIN = 0
IPOL = 0 IEWALD= 0
NTX = 1 NTXO = 1
IG = 71277 TEMPI = 0.00 HEAT = 0.000
NTB = 2 IFTRES= 1 BOXX = 58.586
BOXY = 68.064 BOXZ = 59.311
NRUN = 1 NTT = 1 TEMP0 = 300.000
DTEMP = 0.000 TAUTP = 0.200 TAUTS = 0.200
ISOLVP= 0 VLIMIT= 0.000
NTP = 2 PRES0 = 1.000 COMP = 44.600
TAUP = 0.200 NPSCAL= 0
NTCM = 0 NSCM = 9999999
NSTLIM= 500 INIT = 3 NTU = 1
T = 0.000 DT = 0.00100
NTC = 4 TOL = 0.00050 JFASTW = 0
NTF = 2 NTID = 0 NTNB = 1
NSNB = 25 IDIEL = 1 IMGSLT= 0
IPRR = 0 IPRW = 0 ITRSLU= 1
CUT = 9.000 SCNB = 2.000
SCEE = 1.200 DIELC = 1.000
CUT2ND= 0.00000
NTPR = 25 NTWR = 50 NTWX = 100
NTWV = 0 NTWE = 100 NTWXM = 999999
NTWVM = 999999 NTWEM = 999999 IOUTFM= 0
NTWPRT= 0 NTWPR0= 0
NTR = 0 NTRX = 1
TAUR = 0.00000 NMROPT= 0 ISFTRP= 0
RWELL = 1.00000 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
NATOM = 18452 NRES = 5774
3. ATOMIC COORDINATES AND VELOCITIES
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 5667
Using 5667 waters for fast wat-wat
Solute/solvent pointers:
IPTSOL= 107 NATRCM= 1451
IPTRES= 0 IPTATM= 0
NSPSOL= 10 NSPSTR= 1451
NSOLUT=18452 NATOM =18452
Then, I use the anal fonction for create a pdb file with :
- anal .in :
Exemple et essai pour la fonction ANAL :
1 0 0 0 0 1
0 0 0 0 0
1 0 1 0 0 0
12 2 2 4
0 0 0 0 0 0 0
0 0
PDB
STOP
- md1.xyz
- prmtop.wat
It result a pdb file.
If I look this pdb file with Rasmol (or other), I see this :
wwwwwwwwwwwwwwwwwwwwwwwww ww
wwwwwwwwwwwwwwwwwwwwwwwww ww
wwwwwwwwwwwwwwwwwwwwwwwww ww
wwwwwwwwwwwwwwwwwwwwwwwww ww
wwwwwwPPPPPPPPPwwwwwwwwww ww
wwwwwPPPPPPPPPPPwwwwwwwww ww
wwwwwPPPPPPPPPPPwwwwwwwww ww
wwwwwPPPPPPPPPPPwwwwwwwww ww
wwwwwPPPPPPPPPPPwwwwwwwww ww
wwwwwwPPPPPPPPPwwwwwwwwww ww
wwwwwwwwwwwwwwwwwwwwwwwww ww
wwwwwwwwwwwwwwwwwwwwwwwww ww
wwwwwwwwwwwwwwwwwwwwwwwww ww
|==> empty gap
wwwwwwwwwwwwwwwwwwwwwwwww ww
wwwwwwwwwwwwwwwwwwwwwwwww ww
w = WAT
P = Protein
And if I look pdb files :
after minimization =
------------------
ATOM 1 N ILE 1 19.697 31.112 38.202
ATOM 2 H1 ILE 1 18.710 30.929 38.089
ATOM 3 H2 ILE 1 20.123 31.139 37.286
ATOM 4 H3 ILE 1 20.182 30.374 38.692
ATOM 5 CA ILE 1 19.915 32.406 38.875
ATOM 6 HA ILE 1 19.109 32.568 39.591
ATOM 7 CB ILE 1 21.248 32.398 39.634
ATOM 8 HB ILE 1 21.203 31.593 40.368
ATOM 9 CG2 ILE 1 22.423 32.121 38.690
(....)
after dynamic =
-------------
ATOM 1 N ILE 1 19.904 27.084 35.005
ATOM 2 H1 ILE 1 18.904 26.996 34.889
ATOM 3 H2 ILE 1 20.312 26.823 34.118
ATOM 4 H3 ILE 1 20.280 26.448 35.694
ATOM 5 CA ILE 1 20.237 28.455 35.422
ATOM 6 HA ILE 1 19.564 28.653 36.256
ATOM 7 CB ILE 1 21.656 28.456 35.985
ATOM 8 HB ILE 1 21.747 27.506 36.512
ATOM 9 CG2 ILE 1 22.833 28.412 35.014
(....)
If I look coordonnes, we say that Y and Z are moved
with the same distance for all atom of Protein and WAT.
I look this fact at the first "step" of the dynamic molecular,
at 0.001 ps !
If I change the parameter : NTB = 2 by NTB = 1, I look the
same probleme ! MDIN :
&cntrl
IMIN = 0, IREST = 0, NTX = 1, TEMPI = 0.,
SCEE = 1.2, IDIEL = 1, CUT =9.0,
NTT = 1, TEMP0 = 300.0, TAUTP=0.2,
NTP = 0, TAUP = 0.2,
NTB = 1, NTC = 4, NTF = 2, NSNB = 25,
NSTLIM = 500,
NTWE = 100, NTWX = 50, NTPR = 25,
&end
I would like know why I look this empty gap ?
If I run a molecular dynamic with TEMPI = 0 during a number of
ps, then I arise the temperature to TEMP0 = 300 ant I stay at 300
during a long time, I see the empty gap at the start,
but not at the end !
Witch phenomene produce this effect ???
I would like understand this phenomene.
If I take only WATBOX216, I don't see this phenomene.
In fact, I work on a protease, and I see this phenome only on the Y axis
during
the equilibration. When the temperature stay at 300K during a long
periode,
at the end, I don't observe this empty gap.
--
=========================================================================
Francois Vanelle Tel: +33 (1) 34 65 25 68
Mathematique Informatique et Genomes Fax: +33 (1) 34 65 22 41
Batiment des Biotechnologies Email: vanelle_at_sgi2.jouy.inra.fr
INRA, Jouy-en-Josas, 78352, France
Received on Fri Mar 31 2000 - 01:28:15 PST
