Thanks a lot 4 your reply sir.
I have seen some distortions when i viewed it in VMD.
This is my minimisation input, *min1.in*.
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 YDNA fixed with weak
restraints
10.0
RES 1
20
END
END
*min2.in*
DNA : 10ps MD with res 10 kcal at const
volume
&cntrl
imin =
0,
irest =
1,
ntx =
5,
ntb =
1,
cut =
10,
ntr =
1,
ntc =
2,
ntf =
2,
tempi =
145.83,
temp0 =
300.0,
ntt =
3,
gamma_ln =
1,
nstlim = 50000, dt =
0.001,
ntpr = 500, ntwx = 500, ntwr =
1000,
nmropt =
1,
/
&wt
type = 'TEMP0', istep1 = 1, istep2 =25000, value1 = 145.83, value2 =
300.0,
/
&wt
type='END'
/
Group Input for restrained
atoms
10.0
RES 1
20
END
END
I have done these minimisations only.
The problem of vlimit arises from the first production run output itself.and
with that error the program continues running and the error increases
gradually and get stopped.
>From first MD output itself the error starts.
here is the error
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 = 18000 TIME(PS) = 18.000 TEMP(K) = 102.65 PRESS =
0.0
Etot = -49248.1272 EKtot = 2609.1759 EPtot =
-51857.3032
BOND = 98.5736 ANGLE = 622.0273 DIHED =
568.0625
1-4 NB = 265.7208 1-4 EEL = -5598.8238 VDWAALS =
7905.8834
EELEC = -55768.2035 EHBOND = 0.0000 RESTRAINT =
49.4566
EAMBER (non-restraint) = -51906.7598
Ewald error estimate: 0.6970E-05
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 18001; vmax = 21.0253
vlimit exceeded for step 18007; vmax = 20.6049
vlimit exceeded for step 18011; vmax = 22.0151
vlimit exceeded for step 18012; vmax = 20.7999
vlimit exceeded for step 18046; vmax = 22.3654
vlimit exceeded for step 18047; vmax = 20.6767
vlimit exceeded for step 18050; vmax = 20.0744
vlimit exceeded for step 18087; vmax = 20.3247
vlimit exceeded for step 18096; vmax = 20.1899
NSTEP = 7000 TIME(PS) = 57.000 TEMP(K) = 181.67 PRESS =
0.0
Etot = -45896.5439 EKtot = 4617.8243 EPtot =
-50514.3682
BOND = 123.4178 ANGLE = 673.3129 DIHED =
578.1077
1-4 NB = 259.3839 1-4 EEL = -5552.7593 VDWAALS =
7541.6715
EELEC = -54229.7822 EHBOND = 0.0000 RESTRAINT =
92.2794
EAMBER (non-restraint) = -50606.6476
Ewald error estimate: 0.2620E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 7382; vmax = 21.0734
vlimit exceeded for step 7383; vmax = 27.3836
vlimit exceeded for step 7384; vmax = 20.5762
vlimit exceeded for step 7386; vmax = 20.3252
vlimit exceeded for step 7387; vmax = 21.3863
vlimit exceeded for step 7390; vmax = 20.3066
vlimit exceeded for step 7394; vmax = 20.9089
vlimit exceeded for step 7409; vmax = 20.8912
likewise the error increases from ps to ps and at last it got stopped at
3374ps.
what can I do?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 23 2011 - 01:30:02 PDT
