Hi
I am working on Biomolecular modelling.i have build a model of a biomolecule
and now i am doing MD of that.
I have run the minimisation
My input is
DNA 10ps MD with res 10 kcal/mol restraints
&cntrl
imin =
0,
irest =
0,
ntx =
1,
ntb =
1,
cut =
10,
ntr =
1,
ntc =
2,
ntf =
2,
tempi =
0.0,
temp0 =
150.0,
ntt =
3,
gamma_ln =
1,
nstlim = 50000, dt =
0.001,
ntpr = 500, ntwx = 500, ntwr =
1000,
nmropt =
1,
/
&wt type = 'TEMP0', istep1 = 0, istep2 = 25000, value1 = 0.0, value2 =
150.0,
/
&wt type =
'END'
/
Keep DNA fixed with weak
restraints
10.0
RES 1
20
END
END
But it shows Vlimit exeeding problem aftr some ps.as follows
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -60915.8860 EKtot = 0.0000 EPtot =
-60915.8860
BOND = 46.0249 ANGLE = 545.6061 DIHED =
535.0389
1-4 NB = 259.1070 1-4 EEL = -5583.3665 VDWAALS =
10203.6931
EELEC = -66921.9894 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.2769E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 58.22 PRESS =
0.0
Etot = -51315.5240 EKtot = 1479.8931 EPtot =
-52795.4171
BOND = 75.7294 ANGLE = 599.8928 DIHED =
552.7123
1-4 NB = 272.6463 1-4 EEL = -5596.9545 VDWAALS =
8170.3153
EELEC = -56901.3723 EHBOND = 0.0000 RESTRAINT =
31.6135
EAMBER (non-restraint) = -52827.0306
Ewald error estimate: 0.8510E-04
-----------------------------------------------------------------------
=======
vlimit exceeded for step 10315; vmax = 256.3785
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 4 21 22
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
I have used 1fs instad of 2 fs.then there was difference.But still it shows
vlimit exeeding problem and now the programme got stopped itself.
I have tried different input values.But I cannot tackle the problem.Is that
because the structure is made by model building.?
I have used the inprd structure as the reference structure.
Kindly give me a suggestion.
regrds
Aparna.P
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Received on Thu Sep 22 2011 - 01:30:03 PDT
