Dear Amber users and developers,
I am trying to get the effective born radii for each atom of a molecule when running implicit solvent calculations. For this I am using the rbornstat = 1 flag.
However, it appears that the statistics for the effective Born radii is somehow not properly calculated, with MAX RAD = 0, MIN RAD =999 and AVE RAD and FLUCT =0. Here is what I obtain in my mdout file:
STATISTICS OF EFFECTIVE BORN RADII OVER 100000 STEPS
ATOMNUM MAX RAD MIN RAD AVE RAD FLUCT
1 0.0000 999.0000 0.0000 0.0000
2 0.0000 999.0000 0.0000 0.0000
3 0.0000 999.0000 0.0000 0.0000
4 0.0000 999.0000 0.0000 0.0000
5 0.0000 999.0000 0.0000 0.0000
6 0.0000 999.0000 0.0000 0.0000
7 0.0000 999.0000 0.0000 0.0000
8 0.0000 999.0000 0.0000 0.0000
….
Here is my input file:
MD equilibration with restraints over 200 ps
&cntrl
imin=0, ! Not a minimisation run
irest=1, ! Restart simulation
ntx=5, ! Read coordinates and velocities from coordinate file
nscm=1000, ! Reset COM every 1000 steps
nstlim=100000, dt=0.002, ! Run MD for 200 ps with a timestep of 2 fs
ntpr=500, ntwx=5000, ! Write the trajectory every 10 ps and the energies ev
ioutfm=1, ! Use Binary NetCDF trajectory format (better)
iwrap=0, ! No wrapping will be performed
ntxo=2, ! NetCDF rst file
ntwr=10000, ! Write a restrt file every 10 ps steps, if negative
cut=9999.0, ! Cut-off electrostatics
ntb=0, ! no periodicity
ntc=2, ntf=2, ! SHAKE on all H
ntp=0, ! No pressure regulation
ntt=3, ! Temperature regulation using langevin dynamics
tempi=300.0,
temp0=300.0,
igb=2, ! Implicit solvent
saltcon=0.1, ! Ionic concentration
rbornstat = 1, ! effective Born radii for each atom calculated
gamma_ln=1.0, ! Langevin thermostat collision frequency
ig=-1, ! Randomize the seed for the pseudo-random number gener
ntr=1, ! Flag for restraining specified atoms
restraint_wt=1.0, ! The weight (in kcal/molA2) for the positional restr
restraintmask='.CA', ! String that specifies the restrained atoms
nmropt=0, ! NMR restraints and weight changes read
/
I tried with different molecules but always get the same statistics for the effective radii.
I am using pmemd.cuda from Amber 16.
Is there something wrong with my input file?
Or is there a problem with those calculation?
Is there any other way to calculate the effective Born radius?
Many thanks in advance for your help,
Eric
<
https://mulhollandgroup.wordpress.com/eric-lang/>
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Received on Tue Oct 23 2018 - 08:30:02 PDT
