The starting point of the dragging when using RESTART in steered MD simulation

[li....@gmail.com]

Dear all,

 

I want to use PLUMED to do a steered MD simulation. So far, my simulation has ended (due to time constraints on my supercomputing cluster) after 343.6 ps. Of course, I would like to extend this simulation at time 343.6 ps (see below).

 

  340.0000      1.741399631 RST 1    1.669901492          5.634608620

  340.2000      1.744765544 RST 1    1.669887529          5.638871708

  340.4000      1.743750046 RST 1    1.669873566          5.643257665

  340.6000      1.738023254 RST 1    1.669859604          5.647416165

  340.8000      1.733791092 RST 1    1.669845641          5.651263136

  341.0000      1.727130508 RST 1    1.669831679          5.654779021

  341.2000      1.725282216 RST 1    1.669817716          5.658086585

  341.4000      1.723488285 RST 1    1.669803753          5.661262122

  341.6000      1.722324020 RST 1    1.669789791          5.664434688

  341.8000      1.722597287 RST 1    1.669775828          5.667469834

  342.0000      1.723674306 RST 1    1.669761866          5.670556520

  342.2000      1.720977112 RST 1    1.669747903          5.673595961

  342.4000      1.724568167 RST 1    1.669733940          5.676714926

  342.6000      1.728003740 RST 1    1.669719978          5.679996859

  342.8000      1.728753730 RST 1    1.669706015          5.683355717

  343.0000      1.733390995 RST 1    1.669692053          5.686961999

  343.2000      1.730716765 RST 1    1.669678090          5.690636132

  343.4000      1.729429527 RST 1    1.669664127          5.694139673

  343.6000      1.721055451 RST 1    1.669650165          5.697417495

 

So, I added the 'RESTART' to my CV 1:

 

STEER RESTART CV 1 TO 1.523945954 VEL -0.000139626 KAPPA 4184

 

Here is the restart simulation result:

#! FIELDS time cv1 XX XX RST1 WORK1

  340.0000      1.741413722 RST 1    1.741645542         -0.000000731

  340.2000      1.745491700 RST 1    1.741631580          0.000089639

  340.4000      1.745574130 RST 1    1.741617617          0.000357727

  340.6000      1.741202401 RST 1    1.741603655          0.000465755

  340.8000      1.738295867 RST 1    1.741589692          0.000340891

  341.0000      1.733443640 RST 1    1.741575729         -0.000049119

  341.2000      1.731771580 RST 1    1.741561767         -0.000532700

 

As you can see, the simulation restarts normally. However, the starting point of the dragging in the restart simulation takes as CVs value at 340 ps (~1.74). But I want the starting point of the dragging continues moving in the simulation (i.e. ~1.6699). How can I achieve this matter?

 

I know I can modify the plumed.dat file, e.g. :

 

STEER RESTART CV 1 FROM 1.669901492 TO 1.523945954 VEL -0.000139626 KAPPA 4184

 

However, can the program automatically detect the starting point of the dragging when using RESTART?

 

Best regards,
=========================================
Dechang Li, Ph.D
Biomechanics and Biomaterials Laboratory
Department of Applied Mechanics
School of Aerospace Engineering
Beijing Institute of Technology
Beijing 100081, P. R. China
 
=========================================

[davide branduardi]

Hi Dechang,
As far as I know, the STEER keyword does not support the RESTART keyword.
Best
D
******************************************************
Davide Branduardi,
Postdoc
Theoretical Molecular Biophysics Group
Office 2.255
Max Planck Institute for Biophysics
Max-von-Laue-Straße 3
60438 Frankfurt am Main
Phone: +49 (0)69 63031503
Fax: +49 (0)69 63031502
davide.b...@biophys.mpg.de
davide.b...@gmail.com
Web:
https://sites.google.com/site/davidebranduardi
******************************************************

> --
> You received this message because you are subscribed to the Google Groups
> "PLUMED users" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to plumed-users...@googlegroups.com.
> To post to this group, send email to plumed...@googlegroups.com.
> Visit this group at http://groups.google.com/group/plumed-users?hl=en.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>

[li....@gmail.com]

Hi Davide,

 

Thank you very much for you quick reply!

The STEER keyword does support the RESTART keyword, see manual page 46. I've already used it to restart my steered MD simulation, although the starting point of the dragging is not what I want. I used PLUMED 1.3 with GROMACS 4.5.5.

[Carlo Camilloni]

Hi,

yes this is something that can be considered a bug. Indeed STEER support RESTART, but this only means that the COLVAR file will be appended instead then overwritten. STEERING doesn't write anything but COLVAR and COLVAR is not considered a file from which something can be read. So at present the only thing you can do to restart from the correct position is to read the last value of the centre of the potential from COLVAR and put in plumed using the keyword FROM as you wrote.

Best,

Carlo

[li....@gmail.com]

Oh...., bad news. I think it is not difficult to fix this bug. Can anyone tell me which file should I modify to fix this bug?