[gmx-users] Re: gmx-users Digest, Vol 114, Issue 64

[Santu Biswas]

>
>
>
> "Not working" is too vague a symptom for anyone to guess what the problem
> is, sorry.
>
> Mark
> On Oct 24, 2013 9:39 AM, "Santu Biswas" <santu.biswas85 at gmail.com> wrote:
>
> > dear users,
> >
> >               I am performing 500ps mdrun in vacuum for
> polypeptide(formed
> > by 10-residues leucine) using gromacs_4.5.5(double-precision) using
> > opls-aa/L force field.Input file for 500ps mdrun is given below
> >
> >
> > title                    = peptide in vaccum
> > cpp                    = /lib/cpp
> >
> > ; RUN CONTROL
> > integrator             = md
> > comm_mode        = ANGULAR
> > nsteps                 = 500000
> > dt                        = 0.001
> > ; NEIGHBOR SEARCHING
> > nstlist                  = 0
> > ns_type               = simple
> > pbc                     = no
> > rlist                     = 0
> > ; OUTPUT CONTROL
> > nstxout                  = 1000
> > nstvout                  = 1000
> > nstxtcout               = 0
> > nstlog                    = 1000
> > constraints             = none
> > nstenergy               = 1000
> > ; OPTION FOR ELECTROSTATIC AND VDW
> > rcoulomb                 = 0
> > ; Method for doing Van der Waals
> > rvdw                        = 0
> > ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> > tcoupl                      = V-rescale
> > tc_grps                    = Protein
> > tau_t                        = 0.1
> > ref_t                         = 300
> > gen_vel                    = yes
> > gen_temp                 = 300
> >
> > Using the 500ps trajectory if i run g_hbond_d for calculating the number
> of
> > hydrogen bonds as a function of time using index file(where atom O and
> atom
> > N H is used) it is not working.
> > Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is also
> > not working.
> > I do not know why this is happening.
> >
> > ------
> > santu
> > --
> Thanks Mark for your reply.
>

   Using the 500ps trajectory i want to calculate the number of hydrogen
bonds as a function of time in vacuum .For this calculation i

>  have uesd
> g_hbond_d  -f  traj_0-500ps.trr  -s 500ps.tpr -n index.ndx -num
> hbond-num.xvg -dist dist.xvg -ang angle.xvg
>


> Programm was running .After 1 hour it was still running but there was no
> output.
>

    If I calculate the number of hydrogen bonds as a function of time in
water (no vacuum) using the same command line then there was  no problem.

   Same problem when I used g_rdf in vacuum.The commad line I have used
   g_rdf_4.5.5 -f traj.trr -s 500ps.tpr -n index.ndx -o rdf.xvg and also
checked with -nopbc with the same command line.
   The programm is running but in the output file nothing is written.
   If I used g_rdf in water using the same command line there was no
problem.