[gmx-users] Protein break after simulation

[ISHRAT JAHAN]

how can i check whether the structure is whole or not in .tpr file? After
trjconv whole stage i got broken structure.

On Sun, Sep 10, 2017 at 9:00 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You seem to reporting that your system isn't whole. Is it whole after the
> trjconv -whole stage? Is the structure in that .tpr whole?
>
> Mark
>
> On Sun, Sep 10, 2017 at 9:27 AM ISHRAT JAHAN <jishrat17 at gmail.com> wrote:
>
> > Dear Justin
> > I have used all the commands given in the link provided by you but unable
> > to get the solution.
> > commands used by me are-
> > trjconv -f prtn_full.xtc -s prtn_md.tpr -o prtn_md_whole.xtc -pbc whole
> -n
> > prtn_drg.ndx
> > trjconv -f prtn_md_whole.xtc -s prtn_md.tpr -o prtn_md_cluster.xtc -pbc
> > cluster -n prtn_drg.ndx
> > trjconv -f prtn_md_cluster.xtc -s prtn_md.tpr -o prtn_md_ref.gro -b 0 -e
> 0
> > -n prtn_drg.ndx
> >
> > when i load the prtn_md_ref.gro in vmd i still get the unusual structure
> of
> > protein.
> > Please help me if i did not get the point and also check my full.mdp file
> > whether it is correct or not, given below-
> > ;^M
> > title               =  Yo^M
> > cpp                 =  /usr/bin/cpp^M
> > constraints         =  all-bonds^M
> > integrator          =  md^M
> > dt                  =  0.002    ; ps !^M
> > nsteps              =  50000000 ; total 100000 ps.^M
> > nstcomm             =  100^M
> > nstxout             =  25000^M
> > nstvout             =  500000^M
> > nstfout             =  500000^M
> > nstlog              =  500000^M
> > nstenergy           =  50000^M
> > nstxtcout           =  50000^M
> > xtc-precision       =  10^M
> > nstlist             =  10^M
> > ns_type             =  grid^M
> > rlist               =  0.9^M
> > coulombtype         =  PME^M
> > rcoulomb            =  1.2^M
> > rvdw                =  1.2^M
> > fourierspacing = 0.12^M
> > fourier_nx = 0^M
> > fourier_ny = 0^M
> > fourier_nz = 0^M
> > pme_order = 4^M
> > ewald_rtol = 1e-5^M
> > optimize_fft = yes^M
> > ; Berendsen temperature coupling is on in two groups^M
> > Tcoupl              =  V-rescale^M
> > tc-grps             =  Protein   Non-Protein^M
> > tau_t               =  0.1       0.1^M
> > ref_t               =  310      310^M
> > ; Energy monitoring^M
> > energygrps          =  Protein   Non-Protein
> > ; Isotropic pressure coupling is now on^M
> > Pcoupl              =  berendsen^M
> > Pcoupltype          = isotropic^M
> > tau_p               =  0.5^M
> > compressibility     =  4.5e-5^M
> >
> > 5,1           40%
> > ref_p               =  1.0^M
> > ; Generate velocites is off at 310 K.^M
> > gen_vel             =  no^M
> > gen_temp            = 310^M
> > gen_seed            =  173529^M
> > ^M
> >       Thanks in advance
> >
> >
> >
> >
> > On Sat, Sep 9, 2017 at 7:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 9/9/17 1:50 AM, ISHRAT JAHAN wrote:
> > >
> > >> Dear all,
> > >> I have done 100ns md simulation of protein with drug using
> amber99sb.ff
> > >> with gromacs-5.1.4 version. After simulation i found my protein broken
> > >> into
> > >> smaller parts in .gro file but when i load the final xtc file to
> pr.gro
> > >> molecule does not break. I have applied -pbc nojump ,cluster and whole
> > but
> > >> unable to solve the problem.
> > >> Will anyone help me to solve the above problem.
> > >>
> > >
> > > We'll need to see your commands, exactly as issued, to be able to say
> > > anything. In general:
> > >
> > > http://www.gromacs.org/Documentation/Terminology/Periodic_
> > > Boundary_Conditions#Suggested_trjconv_workflow
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Virginia Tech Department of Biochemistry
> > >
> > > 303 Engel Hall
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalemkul at vt.edu | (540) 231-3129
> > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > >
> > > ==================================================
> > > --
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