[gmx-users] g_hbond and g_rdf in vacuum

[Mark Abraham]

"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
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