Re: [AMBER] TI in vacuum

From: FCUP <Sílvia>
Date: Tue, 8 Feb 2011 16:34:25 +0000

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,
Slvia 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Slvia 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
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