[gmx-users] freeze the particular residues in NPT-NVT

[Justin Lemkul]

On Wed, Mar 20, 2013 at 5:04 AM, 라지브간디 <rajiv at kaist.ac.kr> wrote:

>
>
> Dear gmx,
>
>
> I have used freezgreps for 20 residues of 152 residues contained protein
> and the it took well for energy minimization steps according to the input
> given on mdp and index files. However, when i go for further NPT steps it
> gives following error.
>
>
> Fatal error:
> Group Protein referenced in the .mdp file was not found in the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp.
>
>
> I have rechecked the reference structure (em.gro) with index and nvt.mdp
> files but all of their index numbers are correct. can anyone tell me how
> would avoid them? Thanks in advance.
>
>
The "Protein" group is a default group and should always be present.  The
only reason I can think of that would cause this is if you created an index
file and then deleted the Protein group from it.  If grompp receives an
index file on the command line, the groups provided therein supersede
default groups.

-Justin


>
>
> On Mar 19, 2013, at 11:45 AM, Justin Lemkul wrote:
>
> > On 3/19/13 5:44 AM, ��������������� wrote:
> >> Anyone tell me how do I freeze the particular residues in NPT-NVT
> >> equillibrium steps ? I want them in same conformation as pdb for
> >> further production run ? Thanks in advance
> >>
> >
> > Use freezegrps or strong position restraints.
>
> But note that if you release frozen groups after equilibration your
> system may need further time to equilibrate.
>
> Erik
>
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-- 

========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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