AMBER Archive (2009)

Subject: RE: [AMBER] dipole printing

From: Hemant Kumar (hemant_at_physics.iisc.ernet.in)
Date: Fri Jun 12 2009 - 14:03:17 CDT

Hi Prof Walker,
Thanks for quick reply.
I tried to restainting group with restraintmask and dipole printing with
defining group in &dipoles namelist.
But it seems that when restraintmask is defined program doesn't try to
read any other group information fron input file. as I tried to define
different groups for dipole printing,I got same dipole moments.

With regrads,
Hemant Kumar
Graduate Student
CCMT,Department of Physics
IISC,Bangalore

On Fri, 12 Jun 2009, Ross Walker wrote:

> Hi Hemant,
>
>> I am using polarziable force fields ff02pol.r1.I want to see in my
>> computation
>> "how induced dipole moments are changing with respect to time".
>> Manual suggests that it can be done by using namelist
>> &dipoles,containing the
>> groups whose dipole printing is needed.
>> Now my problem is that I am restrainting a other group(whose dipole
>> printing
>> is not required) also.
>> Is it possible to define other group just for dipole printing which is
>> not used
>> for restaint?
>
> You could try using the newer AMBMASK approach (through restraintmask in the
> cntrl namelist). That way you don't have to specify two sets of the old
> fashioned group input. This might work, although you will need to test it,
> compare with and without the restraints. I wrote this code a long time ago
> and so am not sure if the restriction is just with respect to specifying
> things in the input or whether it is reusing the arrays for the groups
> internally. Thus I would suggest just trying it and see what happens.
>
> Good luck,
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
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