[gmx-users] Re: gmx-users Digest, Vol 114, Issue 75
santu.biswas85 at gmail.com
Mon Oct 28 08:30:48 CET 2013
> > "Not working" is too vague a symptom for anyone to guess what the
> > is, sorry.
> > Mark
> > On Oct 24, 2013 9:39 AM, "Santu Biswas" <santu.biswas85 at gmail.com>
> > > dear users,
> > >
> > > I am performing 500ps mdrun in vacuum for
> > polypeptide(formed
> > > by 10-residues leucine) using gromacs_4.5.5(double-
> > > 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
> > 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
> > > 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
OK - but does your analysis make sense in vacuum?
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.
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