Re: [gmx-users] Conformation search!

On Friday 18 April 2008 10:37 am, Mark Abraham wrote: > Anthony Cruz wrote: > > > You seem to want to let your domains move relative to each other, but > > > > > > also to deny them much internal freedom. So what you want to do is > > > > > > enforce (some of) their internal structure. Thus, u

Re: [gmx-users] Conformation search!

Anthony Cruz wrote: > You seem to want to let your domains move relative to each other, but > also to deny them much internal freedom. So what you want to do is > enforce (some of) their internal structure. Thus, use distance restraints. > > Mark Thank you for your answer. But probab

Re: [gmx-users] Conformation search!

Dear Anthony, You can apply distance restraints to pairs of atoms, e.g. CA atoms in your domains. Check the manual. Ran. Anthony Cruz wrote: > > On Thursday 17 April 2008 9:13 pm, Mark Abraham wrote: > > > Anthony Cruz wrote: > > > > Hi User: > > > > We have a protein with two domains. This two

Re: [gmx-users] Conformation search!

On Thursday 17 April 2008 9:13 pm, Mark Abraham wrote: > Anthony Cruz wrote: > > Hi User: > > We have a protein with two domains. This two domains were connected by > > two linkers of different length. We want to study the different > > conformation that the protein domains can adopt depending the

Re: [gmx-users] Conformation search!

Anthony Cruz wrote: Hi User: We have a protein with two domains. This two domains were connected by two linkers of different length. We want to study the different conformation that the protein domains can adopt depending the length of the linkers without loosing the secondary structure featur

[gmx-users] Conformation search!

Hi User: We have a protein with two domains. This two domains were connected by two linkers of different length. We want to study the different conformation that the protein domains can adopt depending the length of the linkers without loosing the secondary structure feature present. I was think

Re: [gmx-users] Conformation Search with Gromacs

Tandia, Adama wrote: Dear USERS, Can one use Gromacs for conformation search? If yes, how? If you mean systematic search the answer is no. You can do energy minimization or MD. Thanks, Adama _ Adama Tandia Modeling & Simulation Corning INC SP-TD-01-

[gmx-users] Conformation Search with Gromacs

Dear USERS, Can one use Gromacs for conformation search? If yes, how? Thanks, Adama _ Adama Tandia Modeling & Simulation Corning INC SP-TD-01-01 Corning, NY (USA) Tel: 607 248 1036 Fax: 607 974 3405 www.corning.com ___

Re: [gmx-users] conformation search

On Sat, 29 Apr 2006 08:13:33 +0800 "Rongliang Wu" <[EMAIL PROTECTED]> wrote: Hello, gmx-users， is it possible to do conformation searches using gromacs? and how? What do you mean by conformation searches ? XAvier Regards Thanks Rongliang Wu [EMAI

[gmx-users] conformation search

Hello, gmx-users， is it possible to do conformation searches using gromacs? and how? Regards Thanks Rongliang Wu [EMAIL PROTECTED] 　　2006-04-29 ___ gmx-users mailing listgmx-users@gromacs.org