[CPMD-list] Re: two questions about MD

[Axel Kohlmeyer]

On Sun, 25 Feb 2007, qfzhang wrote:

dear zhang,

ZQ> Hi,professor
ZQ>   Thanks for the reply! I still have some question about the constraint force.
ZQ>   Do you mean that the constrain force of one particular distance difference is 
ZQ> just the average of the trajectory, and the barrier can be calculated just by in
ZQ> tegrating such 'averages'?

that is correct, provided the your system is in equilibrium.
please check out the literature about umbrella sampling and
statistical mechanis in general. there are some references 
in the manual and most modern textbooks on MD cover it decently.
there are also a number of alternatives to umbrella sampling 
(which is considered to be rather accurate - if done correctly, 
but quite expensive in terms of cpu time requirements).

ZQ>   Another problem is that the constraint forces in the CONSTRAINT file vary heav
ZQ> ily along the trajectory. Is there some method to solve such a problem? Generall
ZQ> y speaking,how many timestep should be done to get the converged constraint forc
ZQ> e? 

this is to be expected. the instantaneous forces should fluctuate in a 
more-or-less gaussian distribution around the 'true' values and then
you can use conventional statistical measures to judge whether your 
average is converged or not. you also have to balance the accuracy 
of each sampling point against the accuracy of integrating the mean 
forces with a limited number of sampling points. of course the number 
of sampling points depends on the shape of your PMF.

ZQ>   From the example given in cpmd tutorial, when specifing CONSTRAINTS, there is 
ZQ> no NOSE keyword, should that be needed in the constant temperature simulation?
ZQ>    best wishes 

can you please be more specific to which example of what tutorial you 
are referring to. 

cheers,
   axel.


ZQ>                                                        Zhang Qianfan
ZQ>                                                         2007-02-25
ZQ> 
ZQ> Alessandro Curioni д:
ZQ> 
ZQ> > Zhang,
ZQ> > 
ZQ> > 
ZQ> > please use  diagonalization and SCF  for the wfn optimization   ( i.e. add 
ZQ> > LANCZOS DIAGONALIZATION)  when using KPOINTS -
ZQ> > there is a known bug in 3.11.1 for direct optimization (e.g. PCG) and 
ZQ> > k-points. This will be corrected in the new update soon to be for 
ZQ> > distribution.
ZQ> > Regarding the forces  on the costraint : in the file  CONSTRAINTS you have 
ZQ> > the trajectory of the constraint force .....
ZQ> > 
ZQ> > 
ZQ> > 
ZQ> > Alessandro
ZQ> > 
ZQ> > Alessandro CURIONI, PhD
ZQ> > Research Staff Member
ZQ> > Computational Biochemistry and Material Science group
ZQ> > IBM Research Division - Zurich Research Laboratory
ZQ> > Saumerstrasse 4
ZQ> > 8003 Rueschlikon - Switzerland
ZQ> > e-mail: cur at zurich.ibm.com
ZQ> > www:    www.zurich.ibm.com
ZQ> > Tel: +41-1-7248633
ZQ> > Fax: +41-1-7248958
ZQ> > 
ZQ> > 
ZQ> > 
ZQ> > 
ZQ> > "qfzhang" <qfzhang at aphy.iphy.ac.cn> 
ZQ> > Sent by: cpmd-list-bounces at cpmd.org
ZQ> > 02/23/2007 10:22 AM
ZQ> > 
ZQ> > To
ZQ> > cpmd-list at cpmd.org
ZQ> > cc
ZQ> > 
ZQ> > Subject
ZQ> > [CPMD-list] two questions about MD
ZQ> > 
ZQ> > 
ZQ> > 
ZQ> > 
ZQ> > 
ZQ> > 
ZQ> > Hi,expert!
ZQ> >    This is my first time to send email to this mailing list. I have two 
ZQ> > question
ZQ> > s in MD.
ZQ> >    The first one is about BOMD.I want to use k points to simulate the 
ZQ> > crystal sy
ZQ> > stem. but when I specified the keyword MOLECULAR DYNAMICS BO in $CPMD, and 
ZQ> > used 
ZQ> > KPOINTS MONKHORST-PACK, I find that the electronic energy in the loop of 
ZQ> > \\'force 
ZQ> > initialization\\' can never converge.I don\\'t know why. Must I specified some
ZQ>  
ZQ> > speci
ZQ> > al keywords in the input file?
ZQ> >   The second is about the output file CONSTRAINTS. when I get the 
ZQ> > CONSTRAINTS fi
ZQ> > le. How can I get the constraint force? I have fixed the structure of 
ZQ> > distance d
ZQ> > ifference--DIFFER.
ZQ> > 
ZQ> > 
ZQ> >    best wishes
ZQ> >                                                    Qianfan Zhang
ZQ> >                                                     2007-02-23
ZQ> > 
ZQ> > 
ZQ> > _______________________________________________
ZQ> > CPMD-list mailing list
ZQ> > CPMD-list at cpmd.org
ZQ> > http://cpmd.org/mailman/listinfo/cpmd-list
ZQ> > 
ZQ> 
ZQ> 
ZQ> _______________________________________________
ZQ> CPMD-list mailing list
ZQ> CPMD-list at cpmd.org
ZQ> http://cpmd.org/mailman/listinfo/cpmd-list
ZQ> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.