[gmx-users] g_saltbr speed

[Kavyashree M]

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?


Thanks
Kavya

On Thu, Jul 12, 2012 at 5:59 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
> I read that. but while executing tpbconv i did
> not see where i can specify that i do not want
> solvent?
>
> Thanks
> Kavya
>
>
> On Thu, Jul 12, 2012 at 5:47 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 7/12/12 8:15 AM, Kavyashree M wrote:
>>>
>>> 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!
>>>
>>
>> In fact, it's quite easy with tpbconv.  From tpbconv -h:
>>
>> "3. by creating a .tpx file for a subset of your original tpx file, which is
>> useful when you want to remove the solvent from your .tpx file, or when you
>> want to make e.g. a pure Calpha .tpx file. Note that you may need to use
>> -nsteps -1 (or similar) to get this to work. WARNING: this .tpx file is not
>> fully functional."
>>
>>
>> -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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