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From: Francesco Pietra <chiendarret.yahoo.com>

Date: Fri, 24 Aug 2007 09:01:31 -0700 (PDT)

Hi Bud and Ross:

Thanks

When launching the preliminary minimization with adjusted

Initial min for qmmm with dftb

&cntrl

imin=1, maxcyc=500, ncyc=200,

cut=20.0, ntb=0, ntc=2, ntf=2,

ivcap=0, fcap=10, igb=10,

ifqnt=1

/

&qmmm

qmmask=':1',

qmcharge=0,

qmtheory=7,

qmshake=0,

qm_ewald=0

/

sander bombed. min_qmmm_dftb.out ended with:

LOADING THE QUANTUM ATOMS AS GROUPS

Mask :1; matches 98 atoms

SANDER BOMB in subroutine read_qmmm_namelist

qmtheory = DFTB but qmgb > 1. DFTB does not currently

support full QM GB. Only qmgb values of 0 or 1 are supported.

Once flag "qmgb=0" is added just after "qmtheory=7", the minimization is going

on. From tail -f it is at NSTEP 50.

I was unable to detect where GB is stated in the minin. I also wonder about the

difference between "qmgb=0" and qmgb=1" which I did not fin in either Amber9

manual or the pdf included in Marcus Elnster files.

If there is nothing wrong about GB statements, I assume that qmgb=0 (or qmgb=1)

flag should also be added to mdin, modified (for a trial) as follows

300K constant temp for qmmd with dftb

&cntrl

imin=0, ntb=0

cut=20.0, ntc=2, ntf=2,

tempi=300.0, temp0=300.0,

ntt=3, gamma_ln=1.0,

nstlim=1000, dt=0.002,

ivcap=0, fcap=10, igb=10

ntpr=10, ntwx=10,ifqnt=1

/

&qmmm

qmmask=':1',

qmcharge=0,

qmtheory=7,

qmgb=0,

qmshake=0,

qm_ewald=0

/

Thanks

francesco

--- "M. L. Dodson" <mldodson.houston.rr.com> wrote:

*> Francesco Pietra wrote:
*

*> > I am trying to build prmtop and inpcrd for qm-mm with theory=7 (dftb). I am
*

*> > stuck at solvateCap, argument #3 (position).
*

*> >
*

*> > Using *.prepin and *frcmod from previous successful runs with theory=2,
*

*> >
*

*> > startx
*

*> >
*

*> > $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmod/leaprc.ff99
*

*> >
*

*> > source leaprc.gaff
*

*> >
*

*> > loadamberprep EQE.prepin
*

*> >
*

*> > loadamberparams EQE.frcmod
*

*> >
*

*> > check EQE (unit is OK)
*

*> >
*

*> > solvateCap EQE TIP3PBOX EQE 20.0
*

*> >
*

*> > returns
*

*> >
*

*> > Argument #3 is type Unit must be of type: [molecule residue atom list]
*

*> >
*

*> > Using as Argument #3: "1" (residue number in prepin), "C17" (a central
*

*> carbon
*

*> > atom number in prepin, "c" the C17 atom type, or, finally (and blindly)
*

*> > EQE.2.CA the error is: Argument #3 is type String.
*

*> >
*

*> > I am short of imagination (even consulting the manual and the mailing list)
*

*> of
*

*> > what should be given in my case as Argument #3.
*

*>
*

*> Without getting into the structured design of LEaP, perhaps the
*

*> easiest way to for you to proceed is to pick the atom you want to
*

*> make the center of your spherical cap. For purposes of
*

*> illustration, let us assume the Cartesian coordinates of that
*

*> atom are:
*

*>
*

*> x = 1.0, y = 2.0, z = 3.0
*

*>
*

*> Then a solvate cap command using these coordinates might be:
*

*>
*

*> solvateCap EQE TIP3PBOX {1.0 2.0 3.0} 20.0
*

*>
*

*> The desc command is your friend when trying to learn the syntax of
*

*> LEaP. You just have to practice.
*

*>
*

*> > ________________--
*

*> > That said, on summing up info from the manual and suggestions from Bud and
*

*> > Gustavo, I have a number of doubts about min.in and md.in, in particular
*

*> if
*

*> > qm_pme should be omitted at all. The two files I have set up read:
*

*> >
*

*> > Initial min for qmmm with dftb
*

*> > &cntrl
*

*> > imin=1, maxcyc=500, ncyc=200,
*

*> > cut=20.0, ntb=1, ntc=2, ntf=2,
*

*> > ivcap=0, fcap=10
*

*> > ifqnt=1
*

*> > /
*

*> > &qmmm
*

*> > qmmask=':1',
*

*> > qmcharge=0,
*

*> > qmtheory=7,
*

*> > qmshake=0,
*

*> > qm_ewald=0
*

*> > /
*

*> >
*

*> > 300K constant temp for qmmd with dftb
*

*> > &cntrl
*

*> > imin=0, ntb=1
*

*> > cut=20.0, ntc=2, ntf=2,
*

*> > tempi=300.0, temp0=300.0,
*

*> > ntt=3, gamma_ln=1.0,
*

*> > nstlim=20000, dt=0.002,
*

*> > ivcap=0, fcap=10,
*

*> > ntpr=100, ntwx=100,ifqnt=1
*

*> > /
*

*> > &qmmm
*

*> > qmmask=':1',
*

*> > qmcharge=0,
*

*> > qmtheory=7,
*

*> > qmshake=0,
*

*> > qm_ewald=0
*

*> > /
*

*> >
*

*> >
*

*> > I want to try if, at the current implementation of qm-mmm/dftb
*

*> > in Amber9, speed is acceptable for a 98-atoms molecule. If
*

*> > acceptable, to compare ESCF and EPtot with AM1.
*

*> >
*

*>
*

*> Since amber9 sander cannot do pme with QMMM and qmtheory=7, you
*

*> should not turn on qm_pme. Also, for solvent cap simulations,
*

*> ntb=0, not ntb=1 as you have specified. And you should think
*

*> about the suggestion on page 99 of the manual to set igb=10. I
*

*> also think you may have to reduce the timestep. I use 0.5fs for
*

*> QMMM steered MD, but you may be able to get by with 1.0fs, 2.0fs
*

*> is generally workable, but is said to be borderline for classical
*

*> MD. See the email list archives.
*

*>
*

*> Of course the definition of acceptable speed is personal, but I
*

*> have found 90+ atom QM regions to be workable with qmtheory=7.
*

*>
*

*> >
*

*> >
*

*> > Thanks for checking
*

*> >
*

*> > francesco pietra
*

*>
*

*> HTH,
*

*>
*

*> Bud Dodson
*

*> --
*

*> M. L. Dodson
*

*> Email: mldodson-at-houston-dot-rr-dot-com
*

*> Phone: eight_three_two-five_63-386_one
*

*> -----------------------------------------------------------------------
*

*> The AMBER Mail Reflector
*

*> To post, send mail to amber.scripps.edu
*

*> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
*

*>
*

____________________________________________________________________________________

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-----------------------------------------------------------------------

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Received on Sun Aug 26 2007 - 06:07:43 PDT

Date: Fri, 24 Aug 2007 09:01:31 -0700 (PDT)

Hi Bud and Ross:

Thanks

When launching the preliminary minimization with adjusted

Initial min for qmmm with dftb

&cntrl

imin=1, maxcyc=500, ncyc=200,

cut=20.0, ntb=0, ntc=2, ntf=2,

ivcap=0, fcap=10, igb=10,

ifqnt=1

/

&qmmm

qmmask=':1',

qmcharge=0,

qmtheory=7,

qmshake=0,

qm_ewald=0

/

sander bombed. min_qmmm_dftb.out ended with:

LOADING THE QUANTUM ATOMS AS GROUPS

Mask :1; matches 98 atoms

SANDER BOMB in subroutine read_qmmm_namelist

qmtheory = DFTB but qmgb > 1. DFTB does not currently

support full QM GB. Only qmgb values of 0 or 1 are supported.

Once flag "qmgb=0" is added just after "qmtheory=7", the minimization is going

on. From tail -f it is at NSTEP 50.

I was unable to detect where GB is stated in the minin. I also wonder about the

difference between "qmgb=0" and qmgb=1" which I did not fin in either Amber9

manual or the pdf included in Marcus Elnster files.

If there is nothing wrong about GB statements, I assume that qmgb=0 (or qmgb=1)

flag should also be added to mdin, modified (for a trial) as follows

300K constant temp for qmmd with dftb

&cntrl

imin=0, ntb=0

cut=20.0, ntc=2, ntf=2,

tempi=300.0, temp0=300.0,

ntt=3, gamma_ln=1.0,

nstlim=1000, dt=0.002,

ivcap=0, fcap=10, igb=10

ntpr=10, ntwx=10,ifqnt=1

/

&qmmm

qmmask=':1',

qmcharge=0,

qmtheory=7,

qmgb=0,

qmshake=0,

qm_ewald=0

/

Thanks

francesco

--- "M. L. Dodson" <mldodson.houston.rr.com> wrote:

____________________________________________________________________________________

Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out.

http://answers.yahoo.com/dir/?link=list&sid=396545469

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Sun Aug 26 2007 - 06:07:43 PDT

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