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From: M. L. Dodson <mldodson.houston.rr.com>

Date: Fri, 24 Aug 2007 11:17:37 -0500

Francesco Pietra wrote:

* > 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
*

* >
*

I'm sorry, my bad. I forgot that QMMM in amber9 does not support

GB, either. You will not be able to use igb=10. (That is what

specifies a GB simulation.)

Bud

* >
*

* >
*

* > --- "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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*

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*

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*

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*

Date: Fri, 24 Aug 2007 11:17:37 -0500

Francesco Pietra wrote:

is going

about the

Amber9

(or qmgb=1)

I'm sorry, my bad. I forgot that QMMM in amber9 does not support

GB, either. You will not be able to use igb=10. (That is what

specifies a GB simulation.)

Bud

(dftb). I am

mailing list)

Bud and

particular

____________________________________________________________________________________

knows. Yahoo! Answers - Check it out.

-- M. L. Dodson Email: mldodson-at-houston-dot-rr-dot-com Phone: eight_three_two-56_three-386_one ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Sun Aug 26 2007 - 06:07:43 PDT

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