[gmx-users] Are water molecules restrained "by default"?

[Dawid das]

Thank you, but I am still pretty confused. In my *mdp file I use
define = -DPOSRES

and in my *top file there is:

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

now in posre.itp file there are ONLY non-hydrogen atoms of protein.
However after running grompp and using gmxdump to read *trp file I can see:

topology:
   name="RIBONUCLEASE A in water"
   #atoms               = 25205
   #molblock            = 4
   molblock (0):
      moltype              = 0 "Protein_chain_A"
      #molecules           = 1
      #atoms_mol           = 1858
      #posres_xA           = 1858
      posres_xA (1858x3):
         posres_xA[    0]={ 3.10600e+00,  1.16400e+00,  2.92300e+00}
         posres_xA[    1]={ 3.04300e+00,  1.09500e+00,  2.88800e+00}
         posres_xA[    2]={ 3.16400e+00,  1.19800e+00,  2.84900e+00}
         posres_xA[    3]={ 3.16400e+00,  1.12300e+00,  2.99400e+00}
         posres_xA[    4]={ 3.02900e+00,  1.27700e+00,  2.98200e+00}


and ALL of the atoms of the protein. In fact, there are 1858 of them, so
also hydrogen atoms are restrained.
Why? These lines:
#ifdef POSRES
#include "posre.itp"
#endif

are under topology definition of the whole protein:
[ moleculetype ]
; Name            nrexcl
Protein_chain_A     3

[ atoms ]

Although I read documentation on your website I do not understand how I can
create [ moleculetype ] for the non-hydrogen atoms only.

Best wishes,

Dawid Grabarek

2015-07-27 22:25 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 7/27/15 5:18 PM, Dawid das wrote:
>
>> Dear Gromacs Experts,
>>
>> I read in Gromacs documentation that
>> #POSRES_WATER
>> will be interpreted to restrain position of all water oxygen atoms.
>> However
>> if I understand it correctly I should define where proper *itp file is
>> present as it is for restraining heavy atoms of my protein molecule:
>>
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> I neither use #include mechanism for water oxygens nor #define.
>> However I do not get any errors as the documentation suggest when
>> POSRES_WATER is not defined.
>> So my question is whether using this what grompp has generated regarding
>> restraining water oxygens:
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct       fcx        fcy        fcz
>>     1    1       1000       1000       1000
>> #endif
>>
>> is enough to actually restrain those atoms? Or my atoms are not restrained
>> after all?
>> However if they are, how does Gromacs know what atoms are water oxygen
>> atoms? Simply it "recognizes" them because POSRES_WATER flag is used and
>> somewhere in my *top file I include *itp file for water molecues:
>> #include "charmm27.ff/tip3p.itp"
>> ?
>>
>>
> Whether or not restraints are applied is dependent upon what you use in
> the .mdp file with the "define" keyword.  See the manual and basic
> tutorials.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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