[gmx-users] Position restraining of ions.
anu80125 at gmail.com
Thu Jul 16 15:37:41 CEST 2015
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
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
> Alternatively, you can put the
> #ifdef REST_ON
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> 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.
> 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"
>>> should go at the end of POT_rest.itp file and
>>> #ifdef REST_ON
>>> #include "CL_rest.itp"
>>> 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
>>> 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...
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