Hi Tom,
I would like to clarify a few things:
- when the simulatins stops, for example with lamda=0.4, this always occurs
during the minimization process. So, comparing the V0 and V1 outputs:
V0
NSTEP ENERGY RMS GMAX NAME NUMBER
400 -4.5408E+00 3.9275E-04 1.5694E-03 C4 6
BOND = 0.0894 ANGLE = 1.4516 DIHED =
0.0000
VDWAALS = -0.0087 EEL = 4.2609 HBOND =
0.0000
1-4 VDW = -0.0969 1-4 EEL = -10.2371 RESTRAINT =
0.0000
DV/DL = -2.5747
V1
NSTEP ENERGY RMS GMAX NAME NUMBER
400 -4.5408E+00 3.7259E-04 1.5694E-03 C4 6
BOND = 0.0894 ANGLE = 1.4516 DIHED =
0.0000
VDWAALS = -0.0087 EEL = 4.2609 HBOND =
0.0000
1-4 VDW = -0.0969 1-4 EEL = -10.2371 RESTRAINT =
0.0000
DV/DL = -2.5747
Softcore part of the system: 2 atoms, TEMP(K) =
0.00
SC_BOND= 0.0000 SC_ANGLE= 1.9646 SC_DIHED =
0.0000
SC_14NB= -0.2002 SC_14EEL= 0.0000 SC_EKIN =
0.0000
SC_VDW = 0.0000 SC_DERIV= -0.0001
As you can see, the values are equal but in V0 it stops writting before the
line "softcore part of the system:...". In V1, it continues, reaching
minimization at step 422.
The inputs that I'm using for the minimization are:
V0
Minimizacao
&cntrl
imin = 1,
ntx = 1,
maxcyc = 500,
ntpr = 100,
ntmin = 2,
ntf = 1,
ntc = 1,
ntb = 0,
cut = 9.0,
icfe= 1
ifsc= 1
crgmask = ':IMD.H15' (crgmask = ':IML.O17,H19')
scmask= ':IMD.H15' (scmask= ':IML.O17,H19')
clambda = 0.4
&end
The values between parenthesis reflect the changes in the input file V1.
Can you help me understand this?
Thanks in advance,
Sílvia Martins
2011/2/8 <steinbrt.rci.rutgers.edu>
> Hi,
>
> > - where it was lambda=0.4, I change to 0.42, and where it was lambda=0.1,
> > I
> > change to 0.12. In both cases the simulations went well until the end.
>
> to me this indicates that something happens in your structure which causes
> the problem. Changing lambda gives you a slightly different trajectory and
> the problem might then occur at a different point in the trajectory or not
> at all.
>
> > the
> > simulation ran with lambda=0.099....
>
> When you make such tiny changes the potential energy landscape almost
> doesn't change, but again the trajectory will be different after a few
> hundred steps. Is it possible to write out the trajectory after each
> mdstep for both processes at l=0.1 and 0.0999? Then you could compare what
> happens in the first simulation right before it fails compared to the
> second one which works ok.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Sílvia Alexandra Pinto Martins
PhD student
Chemistry Department
Faculty of Sciences
University of Porto
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Received on Tue Feb 08 2011 - 09:00:03 PST
