[gmx-users] Pull code

Michel Cuendet michel.cuendet at epfl.ch
Thu Jan 23 15:31:01 CET 2003


  Thanks for your answer, although it is a bit discouraging. I think 
that code that is "in a bit of disarray" or even "likely horribly 
broken" as you qualify it, should not be part of an official release, 
for the mental sanity of your users. The pull code (as described in the 
manual) was the main reason to choose GROMACS for my project...

  I have however a few additional questions :

1) In case I manage to use 'starting structure' anyway: What kind of 
constraint is applied on the pulled group? Is it determined by the AFM 
'forceconstant' parameter?

2) Concerning the question (3) in my previous email quoted below: Yes, 
the AFM pulling should be at a constant rate - the one specified by 
'pullrate'. But when there is a CMM removal, the position of the spring 
is apparently not properly updated, and the pulling rate resulting in 
the trajectory is different from 'pullrate' - and maybe not even constant.

3) You mention that "GROMACS has been undergoing a lot of development 
recently which makes it harder to work on a feature like the pull code". 
Has version 3.1.4 already undergone those changes? Do they make it 
impossible to repair the pull code?

4) The big question for me now is: is it worth that I try to debug or 
re-implement this myself... Do I have a chance? I need your opinion 
David... I have some experience in programming but I'm by far not an 
expert, especially with big packages.

  Thank you also to David for his suggestion. But I doubt that removing 
degrees of freedom to the system can lead to a good estimate of the free 



Michel Cuendet                            Phone : +41 1 633 4194
Computer-Aided Inorganic Chemistry        Fax   : +41 1 632 1090           
HCI H109
ETH Honggerberg
CH-8093 Zurich
Switzerland                               michel.cuendet at epfl.ch

Justin MacCallum wrote:

>Hi Michel,
>The pull code is currently in a bit of disarray, which is entirely my
>fault. I've been hacking bits and pieces of it as I need to for my work,
>but I haven't had a chance to thoroughly test it. I've been planning to
>do this for quite some time, but I just haven't had a chance. Also,
>GROMACS has been undergoing a lot of development recently which makes it
>harder to work on a feature like the pull code.
>>  I am trying to make free energy measurements for the exchange of a 
>>water molecule around a sodium ion via the Jarzynski method. The 
>>principle is simple, steer a water towards the ion, and integrate the 
>>forces. This system is maybe unusual for gromacs, but according to the 
>>weird trajectories I get, it is doubtfull that the code work correctly 
>>for any system...
>>  Here is a series of questions :
>>1) When all groups are specified, why does mdrun ask for a group? The 
>>group specified here doesen't seem to  influence the results.
>This is a bug thats been fixed in the CVS version. It seems to be
>harmless and everything should still work fine.
>>2) Using AFM, when a group crosses the box boundary, it is replaced b 
>>its image on the other side of the box. But the steering potential stays 
>>centered where it was, which results in an enormous force on the pulled 
>>group, and fast crossing of the box.
>We have used the AFM pulling options quite a lot, but never ran into
>this problem due to the way our system was set up. At some point I would
>like to fix this.
>>3) To prevent this, I decided to remove the center of mass motion of the 
>>ion, and steer the water towards it. But then it apprears that the 
>>effective steering velocity is not correct, as if it was not affected by 
>>the CMM removal.
>I'm not sure what you mean here. The AFM pulling works by moving a
>spring at a constant rate. Currently it doesn't move with the reference
>>3) Using "starting structures", it seems that the translation_rate 
>>parameter is not in nm/step, because the induced translation 
>>unreasonably faster.
>The starting structures option is likely horribly broken. We have
>generally found it easier to insert the molecule of interest and then
>energy minimize (optionally using position restraints or umbrella
>sampling to keep the inserted molecule fixed).
>>4) Using "starting structures", is the constraint also characterized by 
>>the AFM forceconstant parameter?
>>5) Using "starting structures", the steered group doesn't really go to 
>>the reference group, but it passes about 3,5 A from it and continues 
>>further. In which direction?? - "The truth is up there" (Mulder)
>>  Help me out, please, I'm getting nuts with this.
>I hope to be able to improve things sometime in the future. Sorry if
>things aren't working for you.
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