[gmx-users] BUG: Free energy calculation

[Michael Shirts]

Hi, Sabine-

If you can go to http://redmine.gromacs.org/projects/gromacs/issues
and file a bug report (including attaching files), I can look at it.
If that's ends up not working well, you can send me the files off of
the list, but it's usually better to have things in the redmine system
so problems are documented.  I'm also working on the updates to free
energy code in 4.6, so I want to make sure this will be solved there
as well.

Best,
Michael

On Fri, Mar 23, 2012 at 7:16 AM, Sabine Reisser <sabine.reisser at kit.edu> wrote:
> Hi Mark,
>
> with FE, without PR : same error
> without FE, with PR: stable
> without FE, without PR: stable
>
> I've never had this error before.
>
> Logfile says:
> [...]
> Initializing Domain Decomposition on 2 nodes
> Dynamic load balancing: no
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>    two-body bonded interactions: 3.341 nm, LJC Pairs NB, atoms 22476 22761
>  multi-body bonded interactions: 0.649 nm, Angle, atoms 1668 1686
> Minimum cell size due to bonded interactions: 3.675 nm
> Using 0 separate PME nodes
> Optimizing the DD grid for 2 cells with a minimum initial size of 3.675 nm
> The maximum allowed number of cells is: X 1 Y 1 Z 2
> Domain decomposition grid 1 x 1 x 2, separate PME nodes 0
> PME domain decomposition: 2 x 1 x 1
> Domain decomposition nodeid 0, coordinates 0 0 0
> [...]
> Linking all bonded interactions to atoms
> There are 55376 inter charge-group exclusions,
> will use an extra communication step for exclusion forces for PME
>
> The initial number of communication pulses is: Z 1
> The initial domain decomposition cell size is: Z 5.09 nm
>
> The maximum allowed distance for charge groups involved in interactions is:
>                 non-bonded interactions           1.200 nm
>            two-body bonded interactions  (-rdd)   4.213 nm
>          multi-body bonded interactions  (-rdd)   4.213 nm
>
>
>
>
>
> There it stops. In the 1-thread case, the second part is replaced by
> "Initiating Steepest Descents" and then writing out the energies for every
> step.
>
> Gromacs version is 4.5.5.
>
> I also attached the whole logfile.
>
> Cheers
> Sabine
>
>
>
>
>
> On 03/23/2012 11:52 AM, Mark Abraham wrote:
>>
>> On 23/03/2012 9:17 PM, Sabine Reisser wrote:
>>
>>>
>>> Dear gromacs users/developers,
>>>
>>> when trying to couple in a peptide into a membrane with:
>>>
>>> ; Define position restraints for peptide
>>> define          = -DPOSRES
>>>
>>> ; couple in peptide
>>> free_energy     = yes
>>> init_lambda     = 0.05
>>> sc_alpha        = 0.7
>>> sc_power        = 1
>>> couple-moltype  = Protein
>>> couple-lambda0  = none
>>> couple-lambda1  = vdw-q
>>>
>>>
>>> grompp works fine, but mdrun (2 threads) gives me
>>>
>>> Making 1D domain decomposition 1 x 1 x 2
>>> *** glibc detected *** mdrun: realloc(): invalid next size:
>>> 0x00007f0f30305810 ***
>>>
>>> and breaks up.
>>>
>>>
>>> When running "mdrun -nt 1 " on only one thread, it works fine.
>>>
>>> Is this a known bug?
>>>
>>
>> First, is it likely not to be a problem with your setup... is your
>> system stable in parallel without FE code? Without position restraints?
>> What does your .log file say? What GROMACS version is it?
>>
>> Mark
>>
>
>
>
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