Search found 38 matches
- Wed Sep 23, 2009 7:10 pm
- Forum: Simulation setup
- Topic: REMC hippo_input
- Replies: 11
- Views: 42908
Re: REMC hippo_input
Hi, Yes, you need to change the name of the executable in the configure file to hippo_mpi_p3 if you are using that executable. You might have to put ./hippo_mpi_p3 for linux. The configure file just tells mpi where each replica is. Also, you might have to delete the .dat for configure.dat as i can't...
- Tue Sep 22, 2009 2:58 pm
- Forum: Simulation setup
- Topic: cutoff
- Replies: 1
- Views: 10765
Re: cutoff
You can set the cutoff to infinity by setting use_cutoff to zero.
Hope this helps,
Best wishes,
Martin
Hope this helps,
Best wishes,
Martin
- Tue Sep 22, 2009 2:49 pm
- Forum: Simulation setup
- Topic: REMC hippo_input
- Replies: 11
- Views: 42908
Re: REMC hippo_input
Hi,
Unfortunately there is no other way. But for most systems you can just run a single MC simulation at slightly elevated temperatures, this usually gives good sampling.
Best wishes,
Martin
Unfortunately there is no other way. But for most systems you can just run a single MC simulation at slightly elevated temperatures, this usually gives good sampling.
Best wishes,
Martin
- Mon Sep 21, 2009 2:12 pm
- Forum: Simulation setup
- Topic: align principal axis for MD
- Replies: 7
- Views: 18517
Re: align principal axis for MD
Hi,
I can't open your file, sorry. Can you upload again renaming the file ending to .dat. I'll fix the forum so one can upload .txt files asap. Sorry for the inconvenience!
Best wishes,
Martin
I can't open your file, sorry. Can you upload again renaming the file ending to .dat. I'll fix the forum so one can upload .txt files asap. Sorry for the inconvenience!
Best wishes,
Martin
- Mon Sep 21, 2009 2:07 pm
- Forum: Simulation setup
- Topic: REMC hippo_input
- Replies: 11
- Views: 42908
Re: REMC hippo_input
Hi, the temperature from the input file is ignored for REMC. You need to install mpich2 and the daemon needs to be running. Copy all hippo files into directories that have the names of the temperatures. Then use the attached config file to run REMC by executing: >mpiexec -configfile configfile.dat P...
- Fri Sep 18, 2009 2:05 pm
- Forum: Simulation setup
- Topic: align principal axis for MD
- Replies: 7
- Views: 18517
Re: align principal axis for MD
Hi,
Can you send me your input file? I'll have a look, you can attach it to your reply.
Sorry you're having trouble.
Best wishes,
Martin
Can you send me your input file? I'll have a look, you can attach it to your reply.
Sorry you're having trouble.
Best wishes,
Martin
- Fri Sep 18, 2009 11:50 am
- Forum: Simulation setup
- Topic: align principal axis for MD
- Replies: 7
- Views: 18517
Re: align principal axis for MD
Hi,
Yes, the align principle axis works always, 0,1,2,3 are off, x,y,z axes +/- does orientation (i think). You can also set it to align to backbone atoms only. Check the log.txt file for a complete input file, you can take the options from there.
Let me know if this helps!
Best wishes,
Martin
Yes, the align principle axis works always, 0,1,2,3 are off, x,y,z axes +/- does orientation (i think). You can also set it to align to backbone atoms only. Check the log.txt file for a complete input file, you can take the options from there.
Let me know if this helps!
Best wishes,
Martin
- Mon Jul 20, 2009 4:33 pm
- Forum: Simulation setup
- Topic: Replica Exchange Setup
- Replies: 1
- Views: 10888
Re: Replica Exchange Setup
Hi,
Have you installed mpich2 and is the demon running?
I will check again if it runs on our machines and let you know if there's an issue. What machine are you using? We have tested it on Linux and Windows.
Best wishes,
Martin
Have you installed mpich2 and is the demon running?
I will check again if it runs on our machines and let you know if there's an issue. What machine are you using? We have tested it on Linux and Windows.
Best wishes,
Martin
- Tue May 26, 2009 10:10 am
- Forum: Simulation setup
- Topic: Sidetopic : How do you create a primary structure ?
- Replies: 3
- Views: 13492
Re: Sidetopic : How do you create a primary structure ?
Hi,
ACE (acetylate) and AME (amidate) are standard, just add to your sequence:
e.g.
ACE (LALA) AME
Best wishes,
martin
ACE (acetylate) and AME (amidate) are standard, just add to your sequence:
e.g.
ACE (LALA) AME
Best wishes,
martin
- Fri May 22, 2009 9:07 am
- Forum: Simulation setup
- Topic: Sidetopic : How do you create a primary structure ?
- Replies: 3
- Views: 13492
Re: Sidetopic : How do you create a primary structure ?
Hi, Look that the minimizer_cyclical_sequence test job. You can load from sequence. Default is extended structure, but you can also set it helical in the input file. Note the use of 3 and 1 letter side chain identifiers. That is to allow setting the charged state of ionizable residues: e.g. LYS = ch...