PLUMED and DCD files in VMD

[jmw...@gmail.com]

Dear all,

Apologies if this has been posted before (I did look, but no dice).

I recently got involved in running some MD simulations on acemd and wanted to look at some CVs using PLUMED in VMD.

I've installed PLUMED 2.02 and updated VMD to launch with the lastest PLUMED plugin tcl (VMD_plumed-master), all fine so far.

However, when trying to run any sort of script using the plugin in VMD I get the following:

  ERROR in input for command line tool driver : --mf_dcd option is unknown

I noticed that prior to this message the driver informs me that:

The input trajectory can be in any of the following formats:

                 --ixyz - the trajectory in xyz format
                 --igro - the trajectory in gro format

with no mention of .dcd formats but yet it seems that people can happily use .dcd files, indeed, even the example file I tried to use (CREB-CBP binding) had the trajectory in .dcd format (and this of course gave me the same error).

I'd love to know if anyone has come across this problem before and how I can get around it- itching to get started on PLUMED.

Incidentally, I think the install is otherwise OK in so far as i can type plumed --help etc. into the console and bring up the help menu.

Would welcome your thoughts,

Cheers,

James

[Carlo Camilloni]

Hi James,

the possibility of using plumed driver together with many trajectory formats, including dcd, will be available from version 2.1 (that will

be released soon) or using the current master branch of plumed available via github (I would not suggest to use this version for simulations,

but you can probably use it for running your analysis)

Best,

Carlo

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[Toni]

Hi,

Thanks for noting the issue.

It's a PLUMED-GUI problem:  I should point out that it requires Plumed > 2.0 in the installation instructions. 

T

[jmw...@gmail.com]

Thank you both for the feedback.

Would I be correct in thinking then that for now the VMD option is out until then next release, but that the command line version should work with DCDs for now?

Thanks again and best wishes,

James

[Toni Giorgino]

Hi

both will work if you build plumed off the master branch.

In other words, after you

1. install vmd_plumed from  https://github.com/tonigi/vmd_plumed
2. install plumed2 (master branch) from https://github.com/plumed/plumed2

you should have DCD support in the command line and the GUI should work fine with any loaded trajectory.

T

Toni

[jmw...@gmail.com]

Hi Toni,

That's grand, I'll try that out.

Thanks and best wishes,

James

[jmw...@gmail.com]

Happy days, just tried it out and it now works for me.

Thanks again,

James

On Saturday, 21 June 2014 20:43:44 UTC+1, Toni wrote: