[gmx-users] g_saltbr speed

[Kavyashree M]

Dear Sir,

That is true as the number of the frames increased the
memory had almost reached 95% but still it has been in
95% since long and CPU usage drops down to 1.5 -2 %
but in many cases i have seen that still it will run (off course
slowly) and finish. But this was too long. So any suggestions?

Thank you
Kavya

On Thu, Jul 12, 2012 at 3:39 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/12/12 4:51 AM, Kavyashree M wrote:
>>
>> Dear Gromacs users,
>>
>> I was running the saltbridge calculations for a dimeric
>> protein simulation using g_saltbr, But its taking very
>> long time, almost four days still its not completed.
>> Could anyone has suggestion regarding this issue? I am
>> using the same system -
>> Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz
>> where i ran MD. Please give some suggestion as to how to
>> increase the speed of calculation.
>> Command i issued was:
>> g_saltbr -f ../traj.xtc -s md.tpr -t 0.4 -sep
>>
>
> g_saltbr calculates properties of all possible ionic pairs in the system, so
> if there are many, the calculation might take a long time.  Four days sounds
> ridiculous, and perhaps the program has frozen by exhausting the available
> memory.
>
> -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
>
> ========================================
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at
> 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