[gmx-users] Re: Gromacs 4.6 Installation under Cygwin

toma0052 at umn.edu toma0052 at umn.edu
Tue Feb 26 22:11:36 CET 2013

     It looks like the problem might be in my mdp settings. I am using the 
MARTINI force field which uses shift functions for both electrostatics and 
vdw which are only available in the group-based cut-off scheme. OpenMP 
doesn't seem to run with the group-based cut-off scheme, just Verlet.
     If I switch the cut-off scheme to Verlet and change the vdw and 
coulombtype to cut-off and then add in potential-shift-verlet as modifiers 
I can get the system to run. However, in doing this, am I mucking up the 
force field?


On Feb 26 2013, Mirco Wahab wrote:

>Hi Mike
>On 25.02.2013 17:25, toma0052 at umn.edu wrote:
>> ...
>> Estimated maximum distance required for P-LINCS: 0.810 nm
>> ...
>> Domain decomposition grid 4 x 2 x 1, separate PME nodes 0
>Do your runs use PME and/or P-LINCS?
>Maybe you could point out the problem by disabling
>each or both in yout .mdp file?
>I tested some systems (without PME) on cygwin/gmx
>4.6 that worked ok. Probably glitches with the
>cygwin-provided fftw3?
>Maybe you could try to compile fftwf 3.3.3
>in single precision from source and link it to
>your gromacs build.

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