Hi,
I was trying to run md equilibration with belly option (PBC, constant
pressure)on a triplex DNA and the atoms started escaping. Earlier i did a
belly minimisation for 1000 steps (SD). The restart file, when converted
to pdb and viewed also showed signs of water molecules trying to fly
away from the box. please help me out to solve this problem.
Thanks in advance!
Jithesh
------------------------
Here is the input file:
Triplex, initial dynamics w/ belly on DNA, model1, 9.0 cut
&cntrl
timlim = 999999., nmrmax = 1,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 10, ntwx = 500, ntwv = 0, ntwe = 0,
ntwxm = 999999, ntwvm = 999999, ntwem = 999999, ioutfm = 0,
ntwprt = 0,
ntf = 2, ntb = 2, idiel = 1, dielc = 1.0,
cut = 9.0, ntnb = 1, nsnb = 10, ntid = 0,
scnb = 2.0, scee = 1.2, cut2nd = 0.0, ichdna = 0,
ibelly = 1, ntr = 0,
nrun = 1,
nstlim = 12500,
ndfmin = 0, ntcm = 0, nscm = 0,
init = 3, t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 100.0,
ig = 71277, heat = 0.0,
ntt = 1, isolvp = 0, dtemp = 0.0,
tautp = 0.2, tauts = 0.2,
vlimit = 20.0,
tauv0 = 0.0, tauv = 0.1, vzero = 0.0,
ntp = 1, pres0 = 1.0, comp = 44.6,
taup = 0.2, npscal = 1,
ntc = 2, tol = 0.0005,
imgslt = 0, iftres = 1,
jfastw = 0,
&end
&wt
type='TEMP0', istep1=0, istep2=500,
value1=100.0, value2=300.0,
&end
&wt
type='TEMP0', istep1=500, istep2=12500,
value1=300.0, value2=300.0,
&end
&wt
type='END',
&end
&rst
iat=0,
&end
Allowing only the water and counterions to move in the belly
RES 43 3424
END
END
------------------------------------------------------------------------------
a part of the output:
-
KE Trans = 0.2675 KE Rot = 0.4721 C.O.M. Vel = 0.002689
NB-update: NPAIRS = 1731423 HBPAIR = 554480
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 149.11 PRESS
=nan0xFFFFF
Etot = -50544.5142 EKtot = 2988.9982 EPtot = -53533.5124
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 8134.9307
EELEC = -61668.4431 EHBOND = 0.0000 CONSTRAINT = 0.0000
EKCMT = nan0xFFFFFFF VIRIAL = nan0xFFFFFFF VOLUME = 135693.6659
Density = 0.9054
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 0
Energy (this step): Bond = 0.000 Angle = 0.000 Torsion = 0.000
Energy (tot. run) : Bond = 0.000 Angle = 0.000 Torsion = 0.000
DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
This step Entire run This step Entire run
ave. rms ave. rms ave. rms ave. rms
Bond 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Torsion0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
===============================================================================
%SANDER-W-ESCAPE, atom # 0 has escaped
%SANDER-W-ESCAPE, atom # 0 has escaped
%SANDER-W-ESCAPE, atom # 1 has escaped
%SANDER-W-ESCAPE, atom # 1641 has escaped
%SANDER-W-ESCAPE, atom # 1641 has escaped
%SANDER-W-ESCAPE, atom # 1642 has escaped
%SANDER-W-ESCAPE, atom # 1642 has escaped
%SANDER-W-ESCAPE, atom # 1642 has escaped
%SANDER-W-ESCAPE, atom # 1643 has escaped
%SANDER-W-ESCAPE, atom # 1643 has escaped
%SANDER-W-ESCAPE, atom # 1643 has escaped
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Jithesh P.V.
email:jithesh_at_cdac.ernet.in
Received on Fri Feb 04 2000 - 20:53:12 PST
