AMBER Archive (2003)

Subject: RE: ibelly and ntr

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Wed Apr 16 2003 - 14:51:43 CDT

You can take a look at the DNA tutorial on the AMBER website--it has some
discussion of belly/ntr issues that may get you started.

Kristina

>===== Original Message From sychen <yuann_at_bioinfo.ndhu.edu.tw> =====
>Dear Author,
> Is there any reference about the difference between belly simulation
>and position restrain? I'd like to know about the function if them, and
>I don't know why belly is not recommended with EWALD subroutine.
>
>Thank you!
>
>Best Regards,
>
>sychen
>
>
>On Tue, 15 Apr 2003 16:13:11 -0700
>"David A. Case" <case_at_scripps.edu> wrote:
>
>> On Tue, Apr 15, 2003, Youyi Peng wrote:
>>
>> > I can't really understand the differnece between ibelly=1 and ntr=1,
>> > both for frozen /restrained atoms...
>>
>> ibelly=1 are *con*straints: the frozen atoms cannot move at all.
>>
>> ntr=1 are *re*straints: the restrained atoms can move, but won't move far;
>> how far depends on the size of the force constant you use.
>>
>> I'd recommend restraints to keep the backbone (nearly) fixed, but there is
>> no fundamental reason not to use constraints...
>>
>> ..good luck...dac
>>
>> --
>>
>> ==================================================================
>> David A. Case | e-mail: case_at_scripps.edu
>> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>> The Scripps Research Institute | phone: +1-858-784-9768
>> 10550 N. Torrey Pines Rd. | home page:
>> La Jolla CA 92037 USA | http://www.scripps.edu/case
>> ==================================================================

****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu