[gmx-users] strange lincs warning with version 4.6

[Mark Abraham]

2fs is normally considered too large a time step for stable integration
with only bonds to hydrogen constrained, so your observation of
non-reproducible LINCS warnings is not indicative of some other problem.

Also, if you ran your CPU-only calculations with nstlist=25 then AFAIK this
works fine, but is inefficient.

Mark

On Tue, Dec 4, 2012 at 3:41 PM, sebastian <
sebastian.waltz at physik.uni-freiburg.de> wrote:

> 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<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<http://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
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before
>>> posting!
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>> >
>>>
>>>
>>>
>>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>