Search found 38 matches

by martin
Sat Dec 15, 2012 11:10 am
Forum: Installation
Topic: New version
Replies: 3
Views: 10210

Re: New version

Dear John,

Yes, we'll implement that. :)

Cheers,
Martin
by martin
Tue Dec 11, 2012 3:31 pm
Forum: Installation
Topic: New version
Replies: 3
Views: 10210

Re: New version

Hi John,

We were just checking that the upload from our new server works fine. But a new version of hippo is coming out in spring. Is there anything in particular that you are looking for or want fixed?

Best wishes,
Martin
by martin
Thu Oct 20, 2011 2:13 pm
Forum: Running simulations
Topic: rattle: too many constraint iterations.
Replies: 7
Views: 17030

Re: rattle: too many constraint iterations.

Hi, Yes, sigma_membrane is the parameter that sets the hydrophobicity of the membrane, this is somewhat speculative and has to be increased for larger proteins (since it scales with the 'lipid accessible' surface area. If you increase it then at some point your protein should start inserting, -0.03 ...
by martin
Sat Oct 08, 2011 8:25 am
Forum: Running simulations
Topic: rattle: too many constraint iterations.
Replies: 7
Views: 17030

Re: rattle: too many constraint iterations.

Hi, You can do a transrot scan in the implicit membrane. The mode is "transrot scan" And you can control the z, theta (tilt), and phi (rotation) angles by adding the following lines to your input file: zmin (transrot scan) [A] -60 zmax [A] 60 zinf [A] 500 dz [A] 2 dtheta (tilt) [deg] 5 dphi (twist) ...
by martin
Wed Oct 05, 2011 6:32 pm
Forum: Running simulations
Topic: rattle: too many constraint iterations.
Replies: 7
Views: 17030

Re: rattle: too many constraint iterations.

Hi,

Sorry, the implicit membrane is currently only implemented in MC simulation mode. We've demonstrated that it is completely equivalent to MD simulations (it's actually a little faster in terms of sampling per CPU hour). Do you have a protein or a peptide?

Best wishes,
Martin
by martin
Sun Jun 12, 2011 12:30 pm
Forum: Running simulations
Topic: membrane surface tension
Replies: 1
Views: 4771

Re: membrane surface tension

Hi,

Yes, the best option is to increase sigma_membrane. In essence that will increase the hydrophobicity of the bilayer. If you still have problems you can try restraints, will dig it out for you if you need.

Good luck!
Martin
by martin
Thu Oct 01, 2009 4:27 pm
Forum: Simulation setup
Topic: REMC hippo_input
Replies: 11
Views: 16235

Re: REMC hippo_input

Hi, I've looked and not found a solution yet. I think this is an MPI problem, and unfortunately i'm not an expert on MPI. I'll let you know if i have any more suggestions, for the moment i would recommend just running high temperature MC. That is usually quite efficient as well. Good luck! Best wish...
by martin
Thu Oct 01, 2009 4:23 pm
Forum: Simulation setup
Topic: align principal axis for MD
Replies: 7
Views: 6020

Re: align principal axis for MD

Hi,

the bilayer normal is the z-axis, this should be the alignment axis for your peptide if you want to have the system trans-membrane inserted. The membrane is centered on z=0. Hope this helps.
Best wishes,
Martin
by martin
Thu Sep 24, 2009 3:28 pm
Forum: Simulation setup
Topic: REMC hippo_input
Replies: 11
Views: 16235

Re: REMC hippo_input

Yes i think you have to run mdpboot on each node before using mpiexec.
Sorry this is so complicated. MPI is a pain!
Let me know how you fare.
Best wishes,
martin
by martin
Thu Sep 24, 2009 12:53 pm
Forum: Simulation setup
Topic: REMC hippo_input
Replies: 11
Views: 16235

Re: REMC hippo_input

Hi,

Try: /home/peptide/300/hippo_mpi_p3 instead of ./hippo_mpi_p3 for the executable and then change it for each temperature. That should work.
Please let me know if it does. Good luck!
Best wishes,
Martin