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
>>
>
>
>
>
>
____________________________________________________________________________________
> 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
--
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.edu
Received on Sun Aug 26 2007 - 06:07:43 PDT
