[gmx-users] g_saltbr speed

[Kavyashree M]

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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