回复: [AMBER] about MD simulation

From: 廖青华 <fantastic_0919.yahoo.com.cn>
Date: Thu, 12 Mar 2009 00:25:05 +0800 (CST)

Hi Sir, Thanks for your suggestions. I will try to do that. All the best! Qinghua Liao ________________________________ 发件人: Carlos Simmerling <carlos.simmerling.gmail.com> 收件人: AMBER Mailing List <amber@ambermd.org> 已发送: 2009/3/11(周三), 下午6:56:43 主题: Re: [AMBER] about MD simulation I strongly recommend that you read articles in the literature that are similar to what you are trying to do, and see what they did. papers tell you details like # waters in the methods sections. since you haven't told us anything about your system, we don't know if it's reasonable (but 20,000 could easily be ok). I can't stress enough, though, how important it is to read the literature as a source of examples- not just the manual. then you will see whether your goals are practical and readily obtained, or extremely difficult, or somewhere in between. otherwise you will have no idea what to expect. On Wed, Mar 11, 2009 at 5:19 AM, 廖青华 <fantastic_0919@yahoo.com.cn> wrote: > Hi Prof. , > When I add water to the complex using "solvateoct unit TIP3PBOX 8.0" , it > adds nearly twenty thousands water molecules. Is it abnormal? > And somebody suggest me use solvateshell to do that, my queation is that : > is it enough to add solvent only using solvateshell? Thanks! > > All the best! > > Qinghua Liao > > >      ___________________________________________________________ >  好玩贺卡等你发,邮箱贺卡全新上线! > http://card.mail.cn.yahoo.com/ > _______________________________________________ > AMBER mailing list > AMBER@ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER@ambermd.org http://lists.ambermd.org/mailman/listinfo/amber ___________________________________________________________ 好玩贺卡等你发,邮箱贺卡全新上线! http://card.mail.cn.yahoo.com/
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Received on Fri Mar 13 2009 - 01:11:39 PDT
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