[gmx-users] Simulating protein peptide complex

Ruben Cloete ruben at sanbi.ac.za
Tue May 13 10:52:11 CEST 2014


Hi, Justin regarding protein peptide simulation do i prepare the peptide 
as i would a ligand (PRODRG) and add topology to .gro file?

Is there a tutorial for protein protein simulation?

Hope you can assist

Best regards
Ruben


On 26/04/2014 14:50, Justin Lemkul wrote:
>
>
> On 4/26/14, 8:42 AM, Andrew Bostick wrote:
>> Dear Justin
>>
>> Thanks for your reply.
>>
>>
>> This problem can be solved by changing the parameters related to file 
>> system
>> ?
>>
>
> Well, you could, but that would require reformatting your file system 
> for something that can handle file size > 2 GB.
>
>>
>> If I add another RAM to my computer system, my problem solves?
>>
>
> No.
>
> The simplest solutions are what I stated before - reduce your output 
> volume or conduct your runs in shorter intervals of time. This is a 
> very easy limitation to overcome, given the ability to concatenate the 
> output later (obviously on a different machine that supports larger 
> files).
>
> -Justin
>



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