Dear Ross,
thanks a lot for your reply.
It is nice and bad at the same time to know that it is
related to the code and not to the system.
regarding your points:
1. NVT fails in the same way, in face I used the trick of
999999 on a 2nd time to check if it was a pressure/volume
problem, but I obtained several identical failures using
NVT in precedence.
2. unfortunatelly I cannot set ntp=2...because my system
is "really unconventional" and since the gold surface is
made of gold (1 1 1), I had to modify the cell into a
monoclinic (X Y Z 90 90 60)...and ntp=2 does not work for
this case.
3. taup=1 results in a consistent increase of the box
sides...which destroy my system, because as I told you, I
need the ssDNA to have equal spacing in all directions -
and thus also with respect to the periodic images in the
narrow boxes.
I really hope you/anyone in the mailing list will be able
to find some way to prevent this failure, which, however,
curiously
occurs at the restart, not during the run...
looking forward to hear any suggestion
best,
giovanni
On Wed, 9 Nov 2011 09:10:44 -0800
"Ross Walker" <ross.rosswalker.co.uk> wrote:
> Hi Giovanni,
>
>> I am running a simulation on a single C2050 GPU.
>>
>> The system is quite unconventional and composed by 9
>>single strand DNAs
>> attached with a short tiol onto a surface of gold
>>
>> The system is created in order to have an equal spacing
>>between each
>> ssDNA
>> (also in terms of periodic images).
>>
>> To do so the water box is created with 0 buffer in X and
>>Y directions,
>> and
>> with opportune spacing along Z.
>
> I know about this problem but have had it low priority
>to fix since it is
> actually quite useful in identifying people who are
>running too little
> solvent. The issue occurs when the solute touches both
>sides of the box at
> once. This occurs in poorly solvated systems when they
>rotate relative to
> the box or extend during a simulation. As soon as the
>contact occurs the
> kReduceForces error occurs. This is because of some
>assumptions made in the
> code that people would not run such unphysical
>simulations. That said there
> seem to be quite a few people running, as you put it,
>unconventional
> simulations.
>
> I will try and look into this some more and see if I can
>figure out a fix
> for it.
>
>> My input file is below. (# indicates a comment just to
>>make it clear).
>> equil SAM
>> &cntrl
>> imin=0,
>> irest=0,
>> ntx=1,
>> nstlim=5000,
>> dt=0.002,
>> ntc=2,
>> ntf=2,
>> cut=8.0,
>> ntb=2, #the run is
>>actually an NVT,
>> ntp=1, #this trick
>>is used to monitor
>> taup=999999999999999999999999999, #pressure and
>>density
>> ntpr=1000,
>> ntwx=1000,
>> ntt=3,
>> gamma_ln=2.0,
>> temp0=300,
>> ntr=1,
>> ig=-1,
>> iwrap=1,
>> ioutfm=1,
>> /
>> fix surface
>> 10.0
>> RES 1 5445
>> END
>> END
>>
>>
>> END
>
>
>> I need your help, since I don't understand if the
>>problem is related to
>> the
>> system or to some problem with the GPU.
>
> It is a known issue. Can you try a couple of things for
>me please and let me
> know if it still fails.
>
> 1) Try running a true NVT simulation. That is set ntb=1
>and remove the taup.
> I know what you say is a trick to get the density and
>pressure but it runs
> through a lot of additional code and will slow your
>simulation down quite a
> bit vs running true NVT. Note though I still expect this
>calculation to fail
> in the same way.
>
> 2) Try running the simulation as NPT with a reasonable
>taup of say 1.0 or
> so. This I believe should work since the box size should
>expand to prevent
> the contact at the edge of the box. It may just give you
>something crazy
> with your system though since you are at the limits of
>the underlying model.
> Make sure you us anisotropic pressure scaling (ntp=2).
>I'd be interested to
> know if this works while 1 above fails.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor
> |
> | San Diego Supercomputer Center
> |
> | Adjunct Assistant Professor
> |
> | Dept. of Chemistry and Biochemistry
> |
> | University of California San Diego
> |
> | NVIDIA Fellow
> |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/
>|
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk
> |
> ---------------------------------------------------------
>
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Received on Wed Nov 09 2011 - 11:30:03 PST
