[gmx-users] strange lincs warning with version 4.6

[Szilárd Páll]

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).


> 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.

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


> 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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