AMBER Archive (2008)

Subject: Re: AMBER: writing out a distance between two atoms in sander

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Mon Mar 10 2008 - 12:35:58 CDT

Hi Thomas,

Thanks a lot for the precise answer with links in the code. This is
certainly an option... the only problem is that it might work for my
case now but I dont think its an elegant solution. Probably the best
would be an additional namelist parameter which would allow this. Or
something similar to the restraints specification in which one uses a
file to specify which distance (property) to be printed.

Of course, the use of pseudo-restraints I mentioned is still a valid
option (at least I believe so) but unfortunately it cannot be used in
combination with SMD ...

I'll see .. ..

Thanks again
vlad

Thomas Steinbrecher wrote:

> Hi Vlad,
>
> if it is just two atoms that you want to track, I believe you might be
> best served with putting an extra write statement into your sander
> code and recompile a special version of amber just for this job.
>
> The distance you want is calculated at every step anyway, so all you
> would need to do is add a statement to print it out. Go to short_ene.f
> and search for:
>
> !-------------------------------------------------------------
> ! Loop over the 12-6 LJ terms for eedmeth = 1
> !-------------------------------------------------------------
>
> a few lines further down you will see
>
> j = cache_bckptr(im_new)
>
> as far as I know at this point in the code, i and j are atom numbers
> for nonbonded pairs and cache_df(im_new) contains the inverse of their
> distance.
>
> so putting something like this on the next line:
>
> if (i == XXX .and. j == YYY) then
> write (6,'(a,i6,i6,f8.4)') 'distance between: ', i, j,
> 1/cache_df(im_new)
> end if
>
> with XXX and YYY the numbers of the atoms that you want to track
> should print the distance out once per MD step. I haven't tested this
> and obviously its not the *right* way of solving this problem but it
> might work good enough. It puts an if statement into a very important
> loop so it might be very bad for performance. The good thing is that
> this will take care of imaging and the minimum image convention
> automatically. Maybe you have to experiment with the atom numbers for
> a bit, e.g. amber might store them as 3*(actual number-1) or
> something. Start with a test system were you can check the calculated
> distance by hand.
>
> Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
>
> On Mon, 10 Mar 2008, Vlad Cojocaru wrote:
>
>> Dear Amber users,
>>
>> Is there a simple way to make sander output the distnce between two
>> atoms during the MD run without using restraints defined with force
>> constants equal to 0?
>>
>> I am asking because I would like to write out a non-restrained
>> distance much more often than the trajectory frame output. I thought
>> of using the restraints capabilities of sander to defined a
>> pseudo-restraint in which the force constants are all equal to 0 but
>> I am running an SMD simulation in which a different distance is
>> subject to the time-dependent restraint and this type of simulaton
>> only allows 1 restraint to be defined in the RST file.
>>
>> Thanks for any tips
>>
>> Best Wishes
>> Vlad
>>
>> --
>> ----------------------------------------------------------------------------
>>
>> Dr. Vlad Cojocaru
>>
>> EML Research gGmbH
>> Schloss-Wolfsbrunnenweg 33
>> 69118 Heidelberg
>>
>> Tel: ++49-6221-533266
>> Fax: ++49-6221-533298
>>
>> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>>
>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>> ----------------------------------------------------------------------------
>>
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>> Amtgericht Mannheim / HRB 337446
>> Managing Partner: Dr. h.c. Klaus Tschira
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>> http://www.eml-r.org
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-- 
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Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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