[gmx-users] strange lincs warning with version 4.6

[sebastian]

On 11/23/2012 08:29 PM, Szilárd Páll wrote:
> Hi,
>
> On Fri, Nov 23, 2012 at 9:40 AM, sebastian<
> sebastian.waltz at physik.uni-freiburg.de>  wrote:
>
>    
>> Dear GROMCS user,
>>
>> I installed the git gromacs VERSION 4.6-dev-20121117-7a330e6-dirty on my
>> local desktop
>>      
>
> Watch out, the dirty version suffix means you have changed something in the
> source.
>
>
>    
>> (2*GTX 670 + i7) and everything works as smooth as possible. The outcomes
>> are very reasonable and match the outcome of the 4.5.5 version without GPU
>> acceleration. On our
>>      
>
> What does "outcome" mean? If that means performance, than something is
> wrong, you should see a considerable performance increase (PME, non-bonded,
> bondeds have all gotten a lot faster).
>
>    

With outcome I mean the trajectory not the performance.

>    
>> cluster (M2090+2*Xeon X5650) I installed the  VERSION
>> 4.6-dev-20121120-0290409. Using the same .tpr file used for runs with my
>> desktop I get lincs warnings that the watermolecules can't be settled.
>>
>>      
> The group kernels have not "stabilized" yet and there have been some fixes
> lately. Could you please the latest version and check again.
>    

I installed the beta1 release and still the water can not be settled.

> Additionally, you could try running our regression tests suite (
> git.gromacs.org/regressiontests) to see if at least the tests pass with the
> binaries you compiled
> Cheers,
> --
> Szilárd
>
>
>    

Cheers,

Sebastian

>> My .mdp file looks like:
>>
>>   ;
>> title        = ttt
>> cpp                 =  /lib/cpp
>> include             = -I../top
>> constraints         =  hbonds
>> integrator          =  md
>> cutoff-scheme       =  verlet
>>
>> ;define              =  -DPOSRES            ; for possition restraints
>>
>> dt                  =  0.002            ; ps !
>> nsteps              =  100000000              \
>> nstcomm             =  25            ; frequency for center of mass motion
>> removal
>> nstcalcenergy       =  25
>> nstxout             =  100000            ; frequency for writting the
>> trajectory
>> nstvout             =  100000            ; frequency for writting the
>> velocity
>> nstfout             =  100000            ; frequency to write forces to
>> output trajectory
>> nstlog              =  10000            ; frequency to write the log file
>> nstenergy           =  10000            ; frequency to write energies to
>> energy file
>> nstxtcout           =  10000
>>
>> xtc_grps            =  System
>>
>> nstlist             =  25            ; Frequency to update the neighbor
>> list
>> ns_type             =  grid            ; Make a grid in the box and only
>> check atoms in neighboring grid cells when constructing a new neighbor
>> rlist               =  1.4            ; cut-off distance for the
>> short-range neighbor list
>>
>> coulombtype         =  PME            ; Fast Particle-Mesh Ewald
>> electrostatics
>> rcoulomb            =  1.4            ; cut-off distance for the coulomb
>> field
>> vdwtype             =  cut-off
>> rvdw                =  1.4            ; cut-off distance for the vdw field
>> fourierspacing      =  0.12            ; The maximum grid spacing for the
>> FFT grid
>> pme_order           =  6            ; Interpolation order for PME
>> optimize_fft        =  yes
>> pbc            =  xyz
>> Tcoupl              =  v-rescale
>> tc-grps             =  System
>> tau_t               =  0.1
>> ref_t               =  300
>>
>> energygrps          =  Protein Non-Protein
>>
>> Pcoupl              =  no;berendsen
>> tau_p               =  0.1
>> compressibility     =  4.5e-5
>> ref_p               =  1.0
>> nstpcouple        =  5
>> refcoord_scaling    =  all
>> Pcoupltype          =  isotropic
>> gen_vel             =  no;yes
>> gen_temp            =  300
>> gen_seed            =  -1
>>
>>
>> Thanks a lot
>>
>> Sebastian
>> --
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