[gmx-users] implicit solvent concerns

[Albert Solernou]

Thanks for being so clear Mark.

Best,
Albert

On 05/11/2015 03:18 PM, Mark Abraham wrote:
> 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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-- 
---------------------------------
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451