Search found 29 matches
- Mon May 04, 2009 11:47 am
- Forum: Running simulations
- Topic: trouble with MC
- Replies: 11
- Views: 26925
Re: trouble with MC
Hello Martin, after a week of calculations, my MC simulation finished. I proceeded for about 500000000 MC-Steps. Even with this long period, the protein still keeps acting very rigid and stiff (optic control) and I am still wondering, if everything is alright. Only in the last Steps there are some m...
- Wed Apr 22, 2009 9:56 am
- Forum: Analysis
- Topic: How is the helicity calculated ?
- Replies: 4
- Views: 14570
Re: How is the helicity calculated ?
Thanks Jakob,
this helped allot. It was my bad, that I have not understood the range value, which is no completely clear.
I just needed to know how you proceed because I want to use the same criterion on my explicit simulations.
Thanks again for your reply,
your M.Kalavera
this helped allot. It was my bad, that I have not understood the range value, which is no completely clear.
I just needed to know how you proceed because I want to use the same criterion on my explicit simulations.
Thanks again for your reply,
your M.Kalavera
- Tue Apr 21, 2009 10:44 am
- Forum: Running simulations
- Topic: trouble with MC
- Replies: 11
- Views: 26925
Re: trouble with MC
Hi Martin, sorry for the bad formating of my values :oops: but in the normal case the values start proper at column number 41, else wise I get the normal errors for a bad input in the log.txt. What could be a problem is my lag of experience in MC simulations, but I thought that 10*10^6 would be a go...
- Tue Apr 21, 2009 8:07 am
- Forum: Analysis
- Topic: How is the helicity calculated ?
- Replies: 4
- Views: 14570
How is the helicity calculated ?
Hello everybody, my hippo helicity analysis work fine, but I want to understand what is done in the background. Is there a publication or general equation that explains the calculation method ? Actually I don't know how to handle the value "range" in the analysis, because the default state is +-30 d...
- Tue Apr 21, 2009 7:43 am
- Forum: Visualization
- Topic: movie.xyz with vmd
- Replies: 2
- Views: 12004
Re: movie.xyz with vmd
Hi Martin, since yet I have been working with the movie.pdb, but I just got curious about the movie.xyz, because of the small file size and the fact, that your analysis tools use this input as default. So I just wanted to get an inside look for a better understanding of the analysis input. Thx for y...
- Mon Apr 20, 2009 8:34 am
- Forum: Visualization
- Topic: movie.xyz with vmd
- Replies: 2
- Views: 12004
movie.xyz with vmd
Hello everybody, there is a new question about the visualization of the xyz format. If I try to view the movie.xyz in VMD I receive an error message about the first line of the file: "read) ERROR: xyz file 'movie.xyz' should have the number of atoms in the first line." I know, that the *.xyz file's ...
- Thu Apr 16, 2009 12:23 pm
- Forum: Running simulations
- Topic: trouble with MC
- Replies: 11
- Views: 26925
Re: trouble with MC
Here is one of the hippo_input.txt files I use. They are all nearly the same except for the concrete values. There are no additional entries in one off the other input files. hippo input file mode MC simulation input type [PDB,zmx] PDB input file minimized.pdb random number seed (must be < 0) -100 s...
- Thu Apr 16, 2009 8:06 am
- Forum: Running simulations
- Topic: trouble with MC
- Replies: 11
- Views: 26925
Re: trouble with MC
Hi Martin, I tried some new simulations and setups with the same system (GBIM MC and alpha helical protein) we have been talking above. At first, I changed the temperature to the value of 498 K and set the value of prob ridigbodymove to 0.1 .This change showed no effects on the protein behaving. It ...
- Wed Apr 15, 2009 11:48 am
- Forum: Running simulations
- Topic: trouble with MC
- Replies: 11
- Views: 26925
Re: trouble with MC
Hi Martin, I tried the same simulation's with prob rigidbodymove/MC scan set to zero. As you promised, the protein seems to be bound to the starting position and only the sidechains and the backbone is moving. But exactly this is my problem. I just expect the protein to denature or form a random coi...
- Tue Apr 14, 2009 12:15 pm
- Forum: Running simulations
- Topic: trouble with MC
- Replies: 11
- Views: 26925
trouble with MC
Hello everybody, after running several MC simulations in hippo with a nearly perfect helical protein, I tried to interpret the results. As I expected, the protein in an normal GBSA formed a random coil. If you use this coil as a new input for a MC simulation with GBIM you can actually see, that the ...