Re: [ESPResSo-users] Trapping lipids broken?

[Boris Kheyfets]

Any update on trapping lipids in mbtools?

I found that trapped lipids are passed to the trap_mols of /share/espresso/packages/mbtools/utils/misc.tcl which calls

    analyze set trapmol ...

which in turn is defined in tclcommand_analyze_set_parse_trapmol of ESPResSo sources: /src/tcl/topology_tcl.cpp. Reading its code doesn't helped me much: it seems that it calls set_molecule_trap, but I'm not sure.

I re-compiled ESPResSo with MOLFORCES_DEBUG. But it doesn't change the output, so I don't seem to understand how it helps to debug the issue.

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With respect,
Boris, PhD.

On 07/21/2014 04:39 PM, Boris Kheyfets wrote:

Hi all,

trappedlipids.tcl mbtools example script doesn't seem to trap lipids: first three lipids of the system, which are supposed to be trapped, are just swimming all around te membrane. I have compiled ESPResSo with MOLFORCES. I tried to increase the value of trapspring -- but it doesn't help. I also turn on debug messages and see that ESPResSo tries to trap them:


::mbtools::utils > Debug:  applying trap : { 13.5 1.5 8.0 } 0 1000000000 0 { 1 1 1 } {0 0 0} to mol : 0
::mbtools::utils > Debug:  applying trap : { 3.5 11.5 8.0 } 0 1000000000 0 { 1 1 1 } {0 0 0} to mol : 1

::mbtools::utils > Debug:  applying trap : { 7.5 7.5 8.0 } 0 1000000000 0 { 1 1 1 } {0 0 0} to mol : 2

But still it doesn't seem to be working. What could that be?


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Best,

  Boris.