[gmx-users] Position restraining of ions.

[anu chandra]

Thanks for the reply. I have one more quick query about position restrain
here and its about restraining some pat of the whole protein.

Say, I have a protein of 400 aminoacinds ( ie., residues no. 1-400). I
would like to set up position restrain in such way that backbone atoms of
residues 101-200 and 301-400 assign a fixed restrain force of 1000 KJ
through-out the equilibration process and rest of the atoms ( ie, sidechain
atoms of 101-200 and 301-400 and all atoms of residues 1-100 and 201-300)
have descending order of restrain force starting with 1000 KJ, then 500 KJ,
followed by 100 KJ, 50 KJ and finally, 0 KJ. How can I generate such a
position restrain file in Gromcas?

Many thanks in advance

Anu



On Thu, Jul 16, 2015 at 1:38 PM, Gordan Horvat <ghorvat at chem.pmf.hr> wrote:

> I should correct myself. Your top file should work too, because grompp
> assigns certain restraints included in top file to molecules of type
> defined in the first itp file found  above the line that includes these
> restraints.
>
> http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds
>
> Alternatively, you can put the
>
> #ifdef REST_ON
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
> section in your top file below the line that includes the ion group itp
> file, or in the itp file of each ion group you want restrained.
>
> Gordan
>
>
> On 7/16/2015 13:47 PM, Justin Lemkul wrote:
>
>>
>>
>> On 7/16/15 6:22 AM, Gordan Horvat wrote:
>>
>>>   #ifdef REST_ON
>>>   #include "POT_rest.itp"
>>>   #endif
>>>
>>> should go at the end of POT_rest.itp file and
>>>
>>>   #ifdef REST_ON
>>>   #include "CL_rest.itp"
>>>   #endif
>>>
>>> should go at the end of CL.itp file. The restraint you listed
>>> restraints the
>>> first atom of every molecule of the type stated in the corresponding
>>> itp file.
>>> Since potassium and chloride ions are monoatomic, that should work fine.
>>>
>>>
>> Neither of the #ifdefs have to be in the actual .itp files.  They must
>> correspond to the [moleculetype], and since they are appropriately
>> listed consecutively here, this approach works fine.
>>
>>  Elsewise, you can just put the line
>>>
>>>   #include "ionX_rest.itp"
>>>
>>> at the end of the ionX.itp file which will turn on restraints
>>> automatically
>>> without having to define -DPOSIONX keyword in mdp file.
>>>
>>>
>> This is dangerous because then the restraints are *always* on, which is
>> usually undesirable.  If you forget to modify the files if conditions
>> change, then run a long simulation...
>>
>> -Justin
>>
>>
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