Search found 29 matches
- Fri Apr 03, 2009 11:48 am
- Forum: Analysis
- Topic: where is the adiabatic translation+rotation energy scan tool
- Replies: 1
- Views: 9187
where is the adiabatic translation+rotation energy scan tool
Hello everybody, I recognized the possibility of an adiabatic translation+rotation energy scan in hippo. This feature is announced in the wiki-hippo, but I haven't found out if its already implemented or is it an external tool ? In both cases I would like to know where this feature is available and ...
- Thu Mar 12, 2009 9:54 am
- Forum: Visualization
- Topic: Visualization of the membrane
- Replies: 4
- Views: 35507
Re: Visualization of the membrane
Dear denniej0, your script is amazing and it works wonderful in my movie.pdb with VMD. Thanks a lot for your help. The last question I have is referring to the tmemb value you use. You wrote that a tmemb value of 35 would produce an core of 30 Å. Why does't it produce a core with 35 Å ? This is the ...
- Wed Mar 11, 2009 9:46 am
- Forum: Visualization
- Topic: Visualization of the membrane
- Replies: 4
- Views: 35507
Visualization of the membrane
Dear HIPPO users, I'm right now on the search for a possible visualization of the membrane for my GBIM simulations, so that I get an idea where it is in relation to my protein. My first idea was to create a grid or a block in VMD with the help of the draw command in tcl, but I am supposed there are ...
- Fri Mar 06, 2009 10:52 am
- Forum: Running simulations
- Topic: Simulation crash "Command terminated by signal 6"
- Replies: 2
- Views: 15395
Re: Simulation crash "Command terminated by signal 6"
I solved the problem last days on my own. It was a simple problem with the 32.bit version of hippo that crashed every time my outputfiles grew bigger than 2 GB. So I just decreased the rate of the freq_pdb_out value. Now it runs without this problem. The signals are the global "shell signals". In my...
- Thu Feb 26, 2009 3:53 pm
- Forum: Simulation setup
- Topic: Problem with Hippo_input setup for GB/SA
- Replies: 1
- Views: 12821
Re: Problem with Hippo_input setup for GB/SA
I solved my problem,
the entry "use_SSE (0 = slow double prec.) 1" has to be changed to zero instead of one.
the entry "use_SSE (0 = slow double prec.) 1" has to be changed to zero instead of one.
- Wed Feb 25, 2009 1:21 pm
- Forum: Analysis
- Topic: hippo analysis the result
- Replies: 1
- Views: 8749
Re: hippo analysis the result
Hi vkabs, to answer your request for an standard input file: The HIPPO executable comes with a lot of test jobs. One of this jobs is an MD simulation with Generalized Born Implicit-Membrane (GBIM). May be the hippo_input.txt file is a good basis for setting up a new simulation by your self. For a go...
- Wed Feb 25, 2009 11:48 am
- Forum: Simulation setup
- Topic: Problem with Hippo_input setup for GB/SA
- Replies: 1
- Views: 12821
Problem with Hippo_input setup for GB/SA
My problem of today is my NVT MDsimulation with GB/SA conditions. The simulations starts, but I don't receive any values for my Egb or Esasa in my E.dat output file. They are always 0.0000 for every times step. Here is the input file I used. Just have a look and tell me if I make any critical mistak...
- Mon Feb 23, 2009 8:26 am
- Forum: Running simulations
- Topic: Simulation crash "Command terminated by signal 6"
- Replies: 2
- Views: 15395
Simulation crash "Command terminated by signal 6"
Hello, I set up some test simulations based on minimized sequences as input files, but the simulations crashed really early with the following error: "Command terminated by signal 6" "Command terminated by signal 25" What does it mean ? What I found out is, that there is a higher crashing rate for t...
- Wed Feb 11, 2009 3:41 pm
- Forum: Simulation setup
- Topic: Minimization: documentation and constrains ?
- Replies: 0
- Views: 21327
Minimization: documentation and constrains ?
Currently I'm setting up a minimization with an 1 letter code sequence as input. At the moment the minimization works still fine with the example "hippo_input.txt" included in the hippo test job:minimize_cyclical_sequence. But there are still some entries that are not documented in the normal manual...