AMBER Archive (2005)

Subject: Re: RE: AMBER: about run time in GB and PB

From: Yong Xu (yxu_at_mail.sioc.ac.cn)
Date: Thu Apr 21 2005 - 08:17:19 CDT

Dear Prof. Duan and Phineus

thank you for all your reply.
I re-evaluated the time need for MD.
the information shown in my previous mail is the heating process . During that process, I use position constraint to mainchain. when I run production MD, I loose all atom. the speed of MD is about 1/5-1/4 comparing with GB method.

another problem arising.
when I release all atoms without restraint, the RMSD of whole protein reach to 4-6 angstrom within 60ps.
that is to say, the whole system crash.

should I restraint something again, like Ca or mainchain?
is it correct to analysis result using traj with distance-restraint, angle-restraint, or position constraint for some atoms?

Yong

======= 2005-04-21 01:57:00 =======

>This may not be generally true. One needs a bit longer cutoff in GB in
>comparison to explicit solvent with PME. But 15 A is typically ok. If
>you look at the functional form of GB, it drops off pretty quickly. Of
>course, for people who have enough time to burn, extremely long cutoff
>always sounds good.
>
>yong
>
>> whereas for GB one should make the cut-off considerably larger
>(ideally as large as the system itself).
>
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Best regards!
                                 
　　　　　　　　Yong Xu
　　　　　　　　yxu_at_mail.sioc.ac.cn
　　　　　　　　　　2005-04-21
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* Yong Xu
* State Key Lab of Bioorganic & Natural Product Chemistry
* Shanghai Institute of Organic Chemistry
* Chinese Academy of Science
           
* 354 Feng Lin Road, Xu Hui District
* Shanghai, 200032, China
        
* Email: yxu_at_mail.sioc.ac.cn
* yxuemail_at_sina.com
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