Search found 29 matches

by m.kalavera
Mon Jul 20, 2009 4:11 pm
Forum: Simulation setup
Topic: Replica Exchange Setup
Replies: 1
Views: 2064

Replica Exchange Setup

Hello everybody, I want to start a replica exchange simulation (REMC). For this purpose , I took my normal MC hippo_input.txt file and changed MC simulation into REMC simulation. Following the instructions in the manual, I created a file with the name remc_temperature.dat, which consist of 4 lines, ...
by m.kalavera
Thu Jun 18, 2009 1:47 pm
Forum: Analysis
Topic: The Tilt
Replies: 1
Views: 5093

Re: The Tilt

A really great problem has occurred right now: Using the same tool that worked for more than 20 simulations, produces now errors with 20 others which are nearly the same an even MD or MC. The analysis tool writes out the following lines into the z-file: MCstep z tilt kink 0 nan 0.0000 0.0000 10000 n...
by m.kalavera
Thu Jun 18, 2009 9:46 am
Forum: Analysis
Topic: The Tilt
Replies: 1
Views: 5093

The Tilt

hello everybody, I was just wondering, if I got the right idea about the tilt angle, because the paper referenced [13] in the hippo-wikipedia, didn't helped me to understand the method for the tilt-calculation and what is the difference between tilt and kink. The "kink" method seems to be clear, bas...
by m.kalavera
Wed Jun 17, 2009 4:52 pm
Forum: Analysis
Topic: Helicity problem/bug ??
Replies: 0
Views: 9512

Helicity problem/bug ??

Dear Hippos, after allot of simulation runs a very curious point in the helicity analysis came up. I proceeded the my first scans like documented in the hippo manual. My protein is about 40 aa, so I choose aa 2 for the start and aa 38 as the end point. After the analysis, I produced a graphic with g...
by m.kalavera
Tue May 26, 2009 9:50 am
Forum: Simulation setup
Topic: Sidetopic : How do you create a primary structure ?
Replies: 3
Views: 3046

Re: Sidetopic : How do you create a primary structure ?

Is it possible to apply any patches on the terminal residues ?

Greets ,M.kalavera
by m.kalavera
Thu May 21, 2009 9:18 am
Forum: Simulation setup
Topic: Sidetopic : How do you create a primary structure ?
Replies: 3
Views: 3046

Sidetopic : How do you create a primary structure ?

Hello everyone, this is not really an direct question about the simulation setup, but it is connected to in this context. How do you create an simple primary structure of an protein ? Which tools do you use ? I have done some mutations for my protein (secondary structure) with the help of modeller a...
by m.kalavera
Fri May 08, 2009 7:44 am
Forum: Analysis
Topic: Transrotscan: How to use it correctly ?
Replies: 2
Views: 3336

Re: Transrotscan: How to use it correctly ?

Thanks Martin, this explanation helped allot and made it much more clear to me. As you say, the high charge values of my protein could cause the exorbitant and very unrealistic energies and be very troublesome, I will check the whole system with deprotonated residues. This setups are already running...
by m.kalavera
Wed May 06, 2009 9:53 am
Forum: Analysis
Topic: Transrotscan: How to use it correctly ?
Replies: 2
Views: 3336

Transrotscan: How to use it correctly ?

Hello, after a successful MC run, I used the transrot function in Hippo and know some simple questions came up to understand and make it use correctly. How I used it : I created a new folder, copied the hippo executable, oplsa forcefield, movie.pdb and the used hippo_input.txt in it. Afterwards I ju...
by m.kalavera
Wed May 06, 2009 7:18 am
Forum: Running simulations
Topic: trouble with MC
Replies: 11
Views: 5953

Re: trouble with MC

Hello Martin, thx for your reply at first. In my case the protein is a highly charged one and if you say this is causing the trouble, I am ok with it. So I will run my simulations for a much longer time and I will try the replica exchange method. After this is done, I will tell you if and how it wor...
by m.kalavera
Tue May 05, 2009 1:51 pm
Forum: Analysis
Topic: How is the helicity calculated ?
Replies: 4
Views: 2850

Re: How is the helicity calculated ?

Hi everybody, I have a new question again pointing at the helicity. The helicity analysis creates allot of interesting files, as specially the helicity_res.dat. This file contains the helicity in percentage per AA. I assume that this numbers represent the mean value over the whole simulation. Is it ...