[gmx-users] strange vdw energy from rerun with GBSA model.

[Mark Abraham]

On 11/08/2011 10:22 PM, Da-Wei Li wrote:
> Dear Mark and others
>
> I did more tests and thought that it might come from numerical error. 
> The reasons are
>
> 1. If I use .trr file instead of the low precision xtc file, things 
> become better, ie, I get much less snapshots that has high energy.

That doesn't make sense if the underlying frames are the same in your 
.xtc and .trr files. However, if you're talking about different numbers 
of frames, then you probably have transient periodicity artefacts.

>
> 2. I supplied -pforce in my mdrun -rerun and found that the high vdw 
> energy was usually caused by one pair of atoms, whose distance was 
> just very near the clash zone, so that small error on the coordinates 
> would cause large energy error. The force is always around 10000.

Sounds like you have a non-equilibrium trajectory (from your EM?), in 
which case small deviations can have large effects.

>
> 3. Actually bond length and bond angle energies are also affected. I 
> can fully reproduce these two energies if I use .trr file in my rerun 
> but will get several tens of kj/mol error if I use .xtc file, for a 
> protein of size of 100 AA.

Several tens of kJ/mol error in the non-bonded energy looks OK compared 
to the magnitude of the non-bonded energy. Anyway, if your purpose is to 
compare energies computed from the same configurations, then you should 
use the same configurations for computing the energies, not 
approximations to those configurations.

>
>
> Now the question I still have is whether numerical error can be so 
> large? The xtc file has a precision of 0.001 nm. Anyway, I will test 
> more by using double precision Gromacs and define energy groups so 
> that I can compare energy of protein directly between original MD and 
> rerun.
>
>
>
> To Mark only
>
> Thanks. Here it is my script for
>
>  rerun:    mdrun -v -s pbsa.tpr -rerun coor.xtc -e rerun
> superpose:  trjconv -s em.tpr -f coor.xtc -o nojump.xtc -pbc nojump  
> (em.tpr is generated for energy minimization, protein is in the middle 
> of the box)

Here you are generating a nojump trajectory file, but you are not doing 
your rerun on it. That could explain some symptoms - you might not have 
whole molecules.

Mark

>
> rerun .mdp file:
>
> **********************************************************
>
> ; Run parameters
> integrator    = md        ; leap-frog integrator
> nsteps        = 50000000    ; 100 ns
> dt        = 0.002            ; 2 fs
> ; Output control
> nstxout        = 500000    ; save coordinates every 1000 ps
> nstvout        = 500000    ; save velocities every 1000 ps
> nstxtcout    = 5000        ; xtc compressed trajectory output every 1 ps
> nstenergy    = 5000        ; save energies every 1 ps
> nstlog        = 5000        ; update log file every 1 ps
> xtc_grps    = Protein    ; save protein part only
> ; Bond parameters
> continuation    = yes        ; Restarting after NPT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints    = hbonds    ; all bonds (even heavy atom-H bonds) 
> constrained
> lincs_iter    = 1        ; accuracy of LINCS
> lincs_order    = 4        ; also related to accuracy
> ; Neighborsearching
> ns_type        = grid        ; search neighboring grid cels
> nstlist        = 10        ; 20 fs
> rlist        = 0.8        ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 0.8        ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.0        ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype    = cut-off    ; Particle Mesh Ewald for long-range 
> electrostatics
> pme_order    = 4            ; cubic interpolation
> fourierspacing    = 0.12    ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl        = no        ; modified Berendsen thermostat
> tc-grps        = System    ; two coupling groups - more accurate
> tau_t        = 0.1        ; time constant, in ps
> ref_t        = 300         ; reference temperature, one for each 
> group, in K
> ; Pressure coupling is on
> pcoupl        = no        ; Pressure coupling on in NPT
> pcoupltype    = isotropic    ; uniform scaling of box vectors
> tau_p        = 2.0        ; time constant, in ps
> ref_p        = 1.0        ; reference pressure, in bar
> compressibility = 4.5e-5    ; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc        = no        ; 3-D PBC
> ; Dispersion correction
> ;DispCorr    = EnerPres    ; account for cut-off vdW scheme
> DispCorr    = no
> ; Velocity generation
> gen_vel        = no        ; Velocity generation is off
>
>
>
> ; IMPLICIT SOLVENT ALGORITHM
> implicit_solvent         = GBSA
> gb_algorithm             = OBC
> nstgbradii               = 1
> rgbradii                 = 0.8
> gb_epsilon_solvent       = 80
> gb_saltconc              = 0
> gb_obc_alpha             = 1
> gb_obc_beta              = 0.8
> gb_obc_gamma             = 4.85
> gb_dielectric_offset     = 0.009
> sa_algorithm             = Ace-approximation
> sa_surface_tension       = 2.25936
>
> ***************************************************************************************
>
> Thanks all.
>
> dawei
>
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