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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Received on Thu Apr 21 2005 - 09:53:01 PDT
