Re: colvar module question

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Tue Jan 26 2010 - 08:18:15 CST

The only known bug affecting results is the sign error in the angle
gradients, which was already discussed on namd-l last December. If you're
using an "angle" component, you can fix this issue with a negative force
constant (at least until the updated sources are available). As far as we
know, this is the only condition where your trajectory can be affected
(fortunately in a way easy to notice).

All the other fixes are for issues at compilation time with certain
compilers, or errors in the initialization (i.e. the module not allowing you
to run configurations that are otherwise legal). One of these is indeed the
inability to use multiple "run" commands.

Giacomo

---- ----
Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science
    Temple University
    1900 N 12 th Street, Philadelphia, PA 19122
work phone: (+1)-215-204-4216
mobile: (+1)-267-324-7676
mail: giacomo.fiorin_at_gmail.com
---- ----

On Tue, Jan 26, 2010 at 2:32 AM, BIN ZHANG <zhngbn_at_gmail.com> wrote:

> Dear Giacomo:
>
> Thanks a lot for your reply. Now everything makes more sense to me.
>
>
>
> There is a fix coming up on CVS to solve this issue entirely, together with
> several other bugfixes.
>
> For my purpose, the code you posted should be enough for now. I'm only
> using the simple harmonic bias.
>
> But could you be a little bit more specific about these bugfixes? I'm
> planning on using the colvar module to run some productive long
> trajectories, and would like to know whether they are going to affect my
> result or not.
>
>
> Thanks again,
> Bin
>
> In the meantime, depending on what you're doing, you can try by replacing
> the function colvarmodule::finalise() at line 499 of colvarmodule.C with
> what follows.
>
> void colvarmodule::finalise()
> {
> std::string const out_name =
> (output_prefix.size() ?
> std::string (output_prefix+".colvars.state") :
> std::string ("colvars.state"));
> cvm::log ("Saving collective variables state to \""+out_name+"\".\n");
> proxy->backup_file (out_name.c_str());
> std::ofstream out (out_name.c_str());
> out.setf (std::ios::scientific, std::ios::floatfield);
> this->write_restart (out);
> out.close();
>
> cv_traj_os.flush();
> }
>
> This function (as opposed to the one you currently have) will write the
> state file, synchronize the buffer of the trajectory file, but not
> deallocate anything.
>
> This fix will work assuming that you don't need output files written by the
> bias (such as the ".pmf" files written by ABF and metadynamics) at the end
> of each "run" statement. If you do need them, then I can send you all the
> updated sources privately.
>
> Bests
> Giacomo
>
>
> ---- ----
> Giacomo Fiorin
> ICMS - Institute for Computational Molecular Science
> Temple University
> 1900 N 12 th Street, Philadelphia, PA 19122
> work phone: (+1)-215-204-4216
> mobile: (+1)-267-324-7676
> mail: giacomo.fiorin_at_gmail.com
> ---- ----
>
>
> On Mon, Jan 25, 2010 at 4:09 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
>
>> Dear All:
>>
>> I have experienced an interesting behavior of the colvar module. It seems
>> to me that this module does not work properly with the command "run". Say,
>> if I have the following in my config file
>>
>> run 100
>> output ./folder/outfile
>> run 100
>>
>> Then the colvar module will be only initialized correctly in the first 100
>> step. For the next 100 steps, no collective variables are written in either
>> the traj, or state file. It seems the colvar definition are completely
>> uninitialized. This won't cause too much problem, but if you happen to know
>> how to fix it, I would be very happy to listen.
>>
>> Thanks,
>> Bin
>>
>>
>>
>
>

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