[gmx-users] Re: why it is so slow

[Dr. Vitaly Chaban]

I did not follow your previous discussion, but I am sure you need to
quantitatively estimate the slowness of your simulation.

For instance, you can compute the factor by dividing the execution
time using GBSA by the execution time for protein in vacuum.

The people often complain it is slow, whereas it is exactly as it should be.


Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark



On Fri, Nov 2, 2012 at 5:23 PM, Albert <mailmd2011 at gmail.com> wrote:
> Hello Vitaly:
>
> thanks a lot for kind comments.
> Do you have any idea why the running is so slow? Especially considering it
> is with GBSA model and my protein is only with 240 aa.
>
> thank you very much
> best
> Albert
>
> On 11/02/2012 04:30 PM, Dr. Vitaly Chaban wrote:
>>>>
>>>> If I turn this option on, such as:
>>>>
>>>>    pcouple=Isotropic
>>>>
>>>> it is said:
>>>>
>>>>
>>>> ERROR 1 [file eq.mdp, line 78]:
>>>>     Pressure coupling not enough values (I need 1)
>>>>
>>>>
>>>> WARNING 1 [file eq.mdp]:
>>>>     Turning off pressure coupling for vacuum system
>>
>>
>> You canNOT use pressure coupling without PBC in gromacs.
>>
>>
>> Dr. Vitaly V. Chaban
>> MEMPHYS - Center for Biomembrane Physics
>> Department of Physics, Chemistry and Pharmacy
>> University of Southern Denmark
>> Campusvej 55, 5230 Odense M, Denmark
>>
>>
>>