[AMBER] Effective born radii calculations - No correct statistics returned at the end of the mdout file

From: Eric Lang <eric.lang.bristol.ac.uk>
Date: Tue, 23 Oct 2018 15:28:16 +0000

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
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