[gmx-users] implicit solvent concerns

[Mark Abraham]

Hi,

Stuff was probably broken here before 4.6. I would trust only single
threaded in 4.6 and later, and only after comparing with 4.5.

Mark

On Mon, 11 May 2015 14:50 Albert Solernou <a.solernou at leeds.ac.uk> wrote:

> Hi All,
> I am thinking of running an implicit solvent simulation using Gromacs
> (.mdp file pasted at the end of the email). However, I am a bit
> concerned about its accuracy as I get different results for the
> Polarisation term. More specifically, the first step of an energy
> minimisation gives different values for this energy term depending on
> the number of threads/processes that I use (while the rest of the E.
> terms are exactly the same). I tried the Intel compilers + MKL, and the
> GNU compilers + ACML, as well as GMX versions 5.0.4 and 5.1-beta1. I
> could even get a segfault with the GNU compilers and ACML when using 2
> "processes" (gmx mdrun -nt 2).
>
> The question is simple. Am I doing anything wrong? Is there any
> precaution that I should take?
>
> Cheers,
> Albert
>
> -----------------------------------------------
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator    = steep        ; Algorithm (steep = steepest descent
> minimization)
> emtol        = 1000.0      ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> emstep      = 0.01      ; Energy step size
> nsteps        = 50000          ; Maximum number of (minimization) steps
> to perform
>
> ; Parameters describing how to find the neighbors of each atom and how
> to calculate the interactions
> nstlist            = 1            ; Frequency to update the neighbor
> list and long range forces
> cutoff-scheme   = Group
> ns_type            = grid        ; Method to determine neighbor list
> (simple, grid)
> coulombtype        = Cut-Off        ; Treatment of long range
> electrostatic interactions
> rcoulomb        = 999.0        ; Calculate all long range interactions
> rvdw            = 1.2        ; Short-range Van der Waals cut-off
> pbc            = no         ; Periodic Boundary Conditions (yes/no)
>
> ; Implicit solvent parameters:
> implicit-solvent     =  GBSA           ; use implicit solvent
> gb-algorithm         =  OBC           ; use the OBC approach for the GB
> radius
> gb-obc-alpha         =  1           ; parameters correspond to OBC-II
> gb-obc-beta          =  0.8           ;
> gb-obc-gamma         =  4.85           ;
> gb-epsilon-solvent   =  78.5           ; as seen in the original paper.
> sa-algorithm         =  Ace-approximation  ; include surface area
> contribution for non-polar atoms
> sa-surface-tension   =  0.0054           ; default value.
>
> --
> ---------------------------------
>    Dr Albert Solernou
>    EPSRC Research Fellow,
>    Department of Physics and Astronomy,
>    University of Leeds
>    Tel: +44 (0)1133 431451
>
> --
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