Re: [gmx-users] Maximum protein size for REMD?

2013-04-11 Thread Nikunj Maheshwari
I understand the point now. Bigger the system, closer will be the spacing. One thing though: The average energy (mu) returned by the web server for each temperature is 7-8 times more than the actual energy returned after REMD was over. Is there something we are missing here? Thanks. On Tue, Apr

Re: [gmx-users] Maximum protein size for REMD?

2013-04-11 Thread Mark Abraham
Maybe. Either the model in the server is inapplicable for your system, or you've input data for the model incorrectly. Mark On Thu, Apr 11, 2013 at 11:34 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: I understand the point now. Bigger the system, closer will be the spacing. One

[gmx-users] Maximum protein size for REMD?

2013-04-09 Thread Nikunj Maheshwari
Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of research papers, but could not find any protein/peptide above 100 aa related to REMD. We have a protein of 292 aa. Thanks. -- gmx-users mailing

Re: [gmx-users] Maximum protein size for REMD?

2013-04-09 Thread Erik Marklund
I've tried one with 666 aa, but with no publishable results. On 9 Apr 2013, at 09:47, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of

Re: [gmx-users] Maximum protein size for REMD?

2013-04-09 Thread Nikunj Maheshwari
How did you get the final temperature spacing for the run? Did you get the fitted values using polynomial fit? Was the run completed? On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I've tried one with 666 aa, but with no publishable results. On 9 Apr 2013, at 09:47,

Re: [gmx-users] Maximum protein size for REMD?

2013-04-09 Thread Erik Marklund
I used the REMD temperature generator. Needless to say, we got really tight spacing and the enhancement to the sampling was probably small. The whole setup was pretty experimental. The run was completed. Erik On 9 Apr 2013, at 10:01, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: How did

Re: [gmx-users] Maximum protein size for REMD?

2013-04-09 Thread Nikunj Maheshwari
Thats true with our case as well. The spacing was very small, and we got almost 70 replicas for our protein between 280-410K. That's why, we are thinking of any alternate way of getting the spacing, and started using polynomial fit of the average energies we obtained from our first run. Do you

Re: [gmx-users] Maximum protein size for REMD?

2013-04-09 Thread Mark Abraham
On Tue, Apr 9, 2013 at 10:44 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Thats true with our case as well. The spacing was very small, and we got almost 70 replicas for our protein between 280-410K. That's why, we are thinking of any alternate way of getting the spacing, and started