=?GB2312?B?u9i4tDpSZTogW2dteC11c2Vyc10gcG90ZW50aWFsIGVuZXJneQ==?= =?GB2312?B?IG9mIHNwZWNpZmljIGdyb3Vw?=

[Yang Ye]

You can modify your original top's [ molecules ] section to make it only
contains the protein.

On 8/6/2007 4:36 PM, taojinwuhan at sohu.com wrote:
>
>     ----- =D4=AD=CE=C4 -----
>     Dear Yang Ye
>     Thank you very much for your advice!
>     Is any special requirement for this mdp file in step 2 when I make
>     a tpr file?
>     Best regards!
>     Paul
>
>     *From:* Yang Ye <mailto:leafyoung at yahoo.com>
>     *To:* Discussion list for GROMACS users
>     <mailto:gmx-users at gromacs.org>
>     *Subject:* Re: [gmx-users] potential energy of specific group
>     *Sent:* Sun Aug 05 21:47:55 CST 2007
>
>
>
>
>     Hi,
>
>     You shall
>
>     1. Extract the protein coordinates (use trjconv and select groups)
>     from
>     your trajectory file (.xtc).
>     2. Make a .tpr file which only contains protein.
>     3. Use mdrun -rerun to process the trajectory file obtained from 1.
>
>     Regards,
>     Yang Ye
>
>     On 8/5/2007 4:28 PM, taojinwuhan at sohu.com
>     <mailto:taojinwuhan at sohu.com> wrote:
>     >
>     > Hi all,
>     >
>     > I am a freshman in using gromacs. According to my unstanding, the
>     > "potential" in g_energy
>     >
>     > indicates the system's potential energy. Now I want to know the
>     > potential energy of a specific
>     >
>     > group, such as the protein. How should I get it? Could anybody
>     give me
>     > any help ? Thanks a lot!
>     >
>     > Paul
>     >
>     >
>     >
>     >
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