[gmx-users] g_hbond and g_rdf in vacuum

Santu Biswas santu.biswas85 at gmail.com
Thu Oct 24 09:39:08 CEST 2013


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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