[gmx-users] distance restraint in gromacs md run

[Mark Abraham]

Hi,

On Mon, 19 Jun 2017 15:54 Simon Kit Sang Chu <simoncks1994 at gmail.com> wrote:

> Hi Mark,
>
> I thought including distance restraint file here would still be valid?
>

It is valid. I think Justin overlooked how you separated the different
content from different files.

Although this is called POSRES, the file included in not position restraint
> but distance restraint.
>
>
> ; Include distance restraint file
> #ifdef POSRES
> #include "p1p2_dist.itp"
> #endif
>
>
> I try to simulate a trial system and the two chains which are supposed to
> be distance restrained, eventually disassemble. I first
> thought DISPRES could be replaced by POSRES, i.e. the naming is arbitrary.
> It does not seem to be the case.
>

Call it whatever you like, but be consistent. You've spelled the
abbreviations three different ways in this thread.

Right now, I choose "define  = -DDISRES" and "disre = simple". However, the
> message returned indicated that distance restraint is not available in MPI.
> Is that so?
>

Sounds correct. There's many reasons why you don't want to use such ancient
versions of GROMACS. Upgrade the format of the force field files like
Justin has suggested and do everybody a favour ;-)

Mark


Simon
>
> 2017-06-19 19:48 GMT+08:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 6/19/17 1:51 AM, Simon Kit Sang Chu wrote:
> >
> >> Hi,
> >>
> >> I have a protein of interest which requires distance restraint for C
> alpha
> >> atoms. However, the simulation does not seem to include the restraint at
> >> all.
> >>
> >> *prod.mdp*
> >> define              = -DPOSRES
> >> constraints         =  none
> >> integrator          =  md
> >> dt                  =  0.005
> >> nsteps              =  40000000         ; 200 ns
> >>
> >>
> >>
> >> *p1p2-merged.top*
> >>
> >> ; Include forcefield parameters
> >> #include "ffPACE_1.3.itp"
> >>
> >> [ moleculetype ]
> >> ; Name            nrexcl
> >> Protein_A         3
> >>
> >> [ atoms ]
> >> ;   nr       type  resnr residue  atom   cgnr     charge       mass
> typeB
> >>     chargeB      massB
> >>       1         N+      1    MET      N      1        0.7         17   ;
> >> qtot 0.7
> >> .
> >> .
> >> .
> >>   1861  1862  1863  1864     1
> >>
> >> ; Include distance restraint file
> >> #ifdef POSRES
> >> #include "p1p2_dist.itp"
> >> #endif
> >>
> >> *p1p2_dist.itp*
> >> ; distance restraints for r_1-62_r_115-176_&_C-alpha of FullP1P2 in
> water
> >>
> >> [ distance_restraints ]
> >> ;   i     j ? label      funct         lo        up1        up2
>  weight
> >>      2    11 1     0          1   0.283898   0.483898     1.4839
> >> 1
> >>      2    17 1     1          1   0.552993   0.752993    1.75299
> >> 1
> >> .
> >> .
> >> .
> >>
> >>   Do I need to use "define = -DDISTRES" and "ifdef DISPOSRES" instead?
> >>
> >
> > No, because you haven't enclosed your [distance_restraints] in any #ifdef
> > block, so they are always active.
> >
> > Is
> >
> >> distance restraint only used in NMR refinement but not MD?
> >>
> >>
> > No, they can be used during any process.  There are relevant .mdp options
> > that must be set, though (see the manual).
> >
> > How have you determined that the restraints aren't working?
> >
> > -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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