[gmx-users] Re: gmx-users Digest, Vol 114, Issue 64
santu.biswas85 at gmail.com
Sat Oct 26 14:07:59 CEST 2013
> "Not working" is too vague a symptom for anyone to guess what the problem
> is, sorry.
> 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
> > 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
> > hydrogen bonds as a function of time using index file(where atom O and
> > 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
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
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