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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