[gmx-users] g_saltbr speed

[Kavyashree M]

Dear Sir,

I had a problem again during g_saltbr calculation it needs
.xtc and .tpr file, I can reduce the .xtc file to have only
protein but .tpr file will have water also in it. inorder to generate
new tpr file without water using grompp, i need topology file
without water .. so do you suggest me to go this way.. it
appears quite complicated!

Thank you
Kavya

On Thu, Jul 12, 2012 at 4:52 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
> Thanks :). will check whether it makes it faster.
>
> On Thu, Jul 12, 2012 at 4:27 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 7/12/12 6:38 AM, Kavyashree M wrote:
>>>
>>> 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?
>>>
>>
>> http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
>>
>>
>> -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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