Thank you, Phineus
I use cut-off 12 angstrom for GB
and 10 angstrom for PB
when we select GB method, we always say that GB is faster than PB. but it is not as fast as we image, because we must select as possible as large.
since GB have no advantage in speed, we should select PBSA as perfered method.
am I right?
======= 2005-04-21 10:26:00 ：=======
>Dear Yong Xu,
>
>what are the cut-off values in your two simulations? The default cut-off
>for simulation in explicit water
>is 8 angstrom, whereas for GB one should make the cut-off considerably
>larger (ideally as large as the system itself).
>Of course, using a large cut-off with the GB simulation will
>considerably slow down the calculation....
>
>regards,
>Phin.
>
>Yong Xu wrote:
>
>>Dear all
>>
>>I found that on my computer, time used for running GB_MD with com.pdb (protein+ligand = 2700 atoms) is almost same as the time used for running PB_MD with com_water.pdb (protein + ligand + water = 34000 atoms)
>>is this phenomenon normal?
>>
>>
>>Best regard!
>>
>>Yong Xu
>>yxu.mail.sioc.ac.cn
>>2005-04-21
>>
>>===========================================================
>>* 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.mail.sioc.ac.cn
>>* xuyongch.yahoo.com
>>===========================================================
>>
>>
>>
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Best regards!
Yong Xu
yxu.mail.sioc.ac.cn
2005-04-21
===========================================================
* 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.mail.sioc.ac.cn
* yxuemail.sina.com
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Received on Thu Apr 21 2005 - 10:53:00 PDT
