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

[Justin Lemkul]

On 7/28/15 10:00 AM, Dawid das wrote:
> 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.

Those are reference positions for restraints.  The restraints won't be applied 
to anything that's not actually specified in [position_restraints].

> 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.
>

You don't need to.

-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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