[gmx-users] g_saltbr speed

[Kavyashree M]

Dear users,

Its the continuation of the question I asked yesterday, Inorder to reduce
the memory usage during g_saltbr calculations i got the trajectory of only
protein, and tpr file without water and was able to successfully run it. But
unfortunately this again got stopped at 36ns as it had stopped when i was
using the whole trajectory. I tried with -dt 2, still the same problem exists.
Kindly suggest a way out of this situation.

Thank you
With Regards
Kavya


On Thu, Jul 12, 2012 at 6:11 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
> Dear Sir,
>
> Thank you It worked :). a very usefull suggestion.
> But it did not promt to choose any option. I used
> index file.
>
> Thank you
> Kavya
>
> On Thu, Jul 12, 2012 at 6:02 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 7/12/12 8:31 AM, Kavyashree M wrote:
>>>
>>> Ok may be i need to specify an index file. I will try that.
>>> And regarding the WARNING: this .tpx file is not fully functional.
>>> I hope it will work fine enough to finish g_saltbr calculation?
>>>
>>
>> In principle, you should be prompted to choose a default group, but you can
>> also use a custom index group as needed.
>>
>> The warning message is intended to note that the .tpr file you produce will
>> not likely work for running an actual simulation.  It should be fine for
>> analysis.
>>
>>
>> -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
>>
>> ========================================
>>
>>
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