[gmx-users] Gromacs GPU

[Emanuele Coccia]

4.1.1 installed from binaries.

2012/11/21 Justin Lemkul <jalemkul at vt.edu>

>
>
> On 11/21/12 11:11 AM, Emanuele Coccia wrote:
>
>> Running your benchmark for the first time (dhfr-impl-1nm.bench) I have the
>> following message:
>>
>>
>> *Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single
>> precision)
>> *
>> *
>> *
>> *WARNING: OpenMM does not support leap-frog, will use velocity-verlet
>> integrator.*
>> *
>> *
>> *
>> *
>> *WARNING: OpenMM supports only Andersen thermostat with the
>> md/md-vv/md-vv-avek integrators.*
>> *
>> *
>> *
>> *
>> *WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
>>
>> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
>> option.*
>> *
>> *
>> *
>> *
>> *WARNING: The OBC scale factors alpha, beta and gamma are hardcoded in
>> OpenMM with the default Gromacs values.*
>> *
>> *
>> *Floating point exception*
>> *
>> *
>> *
>>
>> *
>> The floating point exception could be due to some other error, I'd be sure
>> that it doesn't depend on the GPU card.
>>
>>
> In theory, the newer card should be fine.  What version of OpenMM are you
> using?
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Emanuele

Università degli Studi dell'Aquila
Dipartimento di Chimica, Ingegneria Chimica e Materiali
CBBC Group - http://bio.phys.uniroma1.it