Re: [gmx-users] about solvate

Rui Li wrote: Dear Mark Thanks for your reply. But I think in the MD process, these original water molecules will move freely, even leave the active site. and the new molecules will replace them. Is it correct? Maybe. Some active sites are closed such that this kind of transition is impossibl

Re: [gmx-users] about solvate

Is it correct? 在您的来信中曾经提到: >From: Mark Abraham <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: Discussion list for GROMACS users >Subject: Re: [gmx-users] about solvate >Date:Thu, 31 May 2007 14:13:34 +1000 > >Rui Li wrote: > > yes,there are som

Re: [gmx-users] about solvate

ion list for GROMACS users >To: Discussion list for GROMACS users >Subject: Re: [gmx-users] about solvate >Date:Thu, 31 May 2007 14:13:34 +1000 > >Rui Li wrote: > > yes,there are some water molecules embedded in an enzyme active site.If I remove > > them,and use genbox to get

Re: [gmx-users] about solvate

et new water molecules , Does it influence the simulation result? 在您的来信中曾经提到: >From: Mark Abraham <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: Discussion list for GROMACS users >Subject: Re: [gmx-users] about solvate >Date:Thu, 31 May 2007 00:

Re: [gmx-users] about solvate

Rui Li wrote: yes,there are some water molecules embedded in an enzyme active site.If I remove them,and use genbox to get new water molecules , Does it influence the simulation result? Of course! If you have any appreciation for how enzymes work, you'll quickly realise that anything in the ac

Re: [gmx-users] about solvate

;To: Discussion list for GROMACS users >Subject: Re: [gmx-users] about solvate >Date:Thu, 31 May 2007 00:16:37 +1000 > >Rui Li wrote: > > Dear gmx-users: > > > > I get a pdb file,and there are some water moleculers included in it. > > Should I remove these wate

Re: [gmx-users] about solvate

Rui Li wrote: Dear gmx-users: I get a pdb file,and there are some water moleculers included in it. Should I remove these water moleculers before I use genbox? Depends what those waters are doing. Waters embedded in an enzyme active site should probably stay... but of course with such a syst

[gmx-users] about solvate

Dear gmx-users: I get a pdb file,and there are some water moleculers included in it. Should I remove these water moleculers before I use genbox? Any reply is appreciated. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mail