Hi Rui Li, That depends on the time scale...
Tsjerk On 5/31/07, Rui Li <[EMAIL PROTECTED]> 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? 在您的来信中曾经提到: >From: Mark Abraham <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >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 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 active site is finely tuned for > being there. If you don't know how enzymes work in general, don't > simulate them without reading a lot of literature on simulating enzyme > mechanisms. > > I cannot imagine a reason why you would want to remove such waters and > rely on genbox to insert a random number of water molecules depending on > steric clashes between arbitrarily placed atomic boundaries. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
