Re: FATAL ERROR: Setting parameter constraints from script failed!

From: Do Nhu Trang (dntrang_at_gmail.com)
Date: Fri Jan 09 2009 - 08:31:02 CST

Thanks so much for the suggestions.
The protocol of Joshua works well with the constraints on whole system with
the same force and the constraints decrease uniformly as he said. But my
case is a little bit different. I need to apply the constraints to a part of
the system and the time of different constraints are different.
So now, the easiest way I found is splitting the simulation into stages.
However, by doing so, I have problem in watching the whole evolution of the
trajectories.
I still need a more graceful and efficient way. Any more suggestion?

Bests,
Trang.

On 1/8/09, Joshua Adelman <jadelman_at_berkeley.edu> wrote:
>
> Hi Trang,
>
> I find a simple way to do this is to set up a constraint file with the
> force constants set to 1.0 (usually in the beta column). Let's say that I
> want to start the constraints (restraints) at 5.0 kcal/mol/A^2. I use the
> following script at the end of my file to gradually decrease the
> constraints:
>
> constraints on
> consref ../xxx_protrestraint.pdb
> conskfile ../xxx_protrestraint.pdb
> conskcol B
>
>
> #protocol
>
> set k_init 5.0
>
> for {set i 0} {$i <= 10} {incr i 1} {
> set ck [expr {$k_init - $i*0.5}]
> constraintScaling $ck
> run 25000
> }
>
> This protocol assumes that you're restraining all of your atoms with the
> same force and that you want to decrease them uniformly.
>
> Josh
>
>
>
> On Jan 8, 2009, at 8:58 AM, Axel Kohlmeyer wrote:
>
> On Thu, 8 Jan 2009, Do Nhu Trang wrote:
>>
>> DNT> Dear all,
>>
>> dear trang,
>>
>> DNT> I would like to perform a simulation with restraints released
>> gradually. I
>> DNT> want to control several phases in one configuration file. The
>> procedure I
>>
>> if i remeber correctly, NAMD doesn't handle this scenario very
>> gracefully. you better be using multiple input files. there is
>> next to no gain from having this in one script anyways.
>>
>> cheers,
>> axel.
>>
>>
>> DNT> have done is the following:
>> DNT>
>> DNT> 1. turn on the constraints
>> DNT> 2. specify the reference pdb file together with force constant
>> DNT> 3. run for a number of timesteps
>> DNT> 4. turn off the constraints
>> DNT> 5. turn on again with another reference pdb file and force constant
>> DNT> 6. run for another number of timesteps
>> DNT> ...
>> DNT> The detail script of this part is attached below. After running for
>> the
>> DNT> first number of steps (20000 in this case), NAMD stops running and
>> reports
>> DNT> this following error:
>> DNT> "TCL: Setting parameter constraints to off
>> DNT> FATAL ERROR: Setting parameter constraints from script failed!"
>> DNT>
>> DNT> I found the similar problem reported by Marc vander Kamp a long time
>> ago
>> DNT> http://www-s.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1095.html
>> DNT> but there is still no reply to this message. I would like to ask Marc
>> if he
>> DNT> could already solve this problem, and I also need help from all NAMD
>> users.
>> DNT>
>> DNT> Many thanks.
>> DNT> Trang.
>> DNT>
>> DNT> #####################
>> DNT>
>> DNT> constraints on
>> DNT> consref K_18_restrained_5.pdb
>> DNT> conskfile K_18_restrained_5.pdb
>> DNT> conskcol B
>> DNT> run 20000;
>> DNT> constraints off;
>> DNT>
>> DNT> constraints on;
>> DNT> consref K_18_restrained_3.pdb;
>> DNT> conskfile K_18_restrained_3.pdb;
>> DNT> conskcol B;
>> DNT> run 5000;
>> DNT> ..........
>> DNT>
>>
>> --
>> =======================================================================
>> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
>> Center for Molecular Modeling -- University of Pennsylvania
>> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
>> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
>> =======================================================================
>> If you make something idiot-proof, the universe creates a better idiot.
>>
>>
>
> ------------------------------------------------------------------------------------------------------
> Joshua L. Adelman
> Biophysics Graduate Group Lab: 510.643.2159
> 218 Wellman Hall Fax: 510.642.7428
> University of California, Berkeley
> http://nature.berkeley.edu/~jadelman>
> Berkeley, CA 94720 USA
jadelman_at_berkeley.edu
>
> ------------------------------------------------------------------------------------------------------
>
>
>
>

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