[gmx-users] Re: gmx-users Digest, Vol 114, Issue 75

[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
>
>
With what groups? Can there be any hydrogen bonds between those groups?

Is there a bug fixed in a version of g_hbond that isn't 2 years old? Did a
shorter trajectory work because it took less time? Does doing only one of
three analyses help things to work? You'd be much closer to a solution if
you'd tried some simplifications and done some detective work already ;-)


> > 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.
>


RDF of what, in vacuum? What groups did you use?


>    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.
>

OK - but does your analysis make sense in vacuum?

Mark

Thanks Mark for your reply


In the index file I mentioned C=O oxygen atom and N-H hydrogen atom. Now I
want to calculate the distance between O atom and N-H hydrogen atom using
g_rdf in vacuum.


Similarly using the same index file I want to calculate the number of
hydrogen bonds as a function of time in vacuum using g_hbond.
Yes there is a H bond between C=O oxygen atom of i-th residue and N-H
hydrogen of i+4-th residue.
 I also checked with shorter trajectory there is also same problem .

Please let me know If there are any mistakes.

-----
santu