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Bug in masses passed to namd #162

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GiovanniBussi opened this issue Jul 16, 2015 · 1 comment
Closed

Bug in masses passed to namd #162

GiovanniBussi opened this issue Jul 16, 2015 · 1 comment
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@GiovanniBussi
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See this thread:
https://groups.google.com/d/msgid/plumed-users/07f2a653-af03-42f6-905a-04c66da0679e%40googlegroups.com

Notice that since commit 73c5c8f (which is in 2.1.0 but not in 2.0.x) masses are taken into account by PLUMED only at the first step. I suspect that the masses passed after the first step are correct. This could mean that:

  1. In PLUMED 2.0 masses were wrong only at the first step
  2. Since PLUMED 2.1 masses are wrong during the whole simulation.
    Perhaps that's why we did not notice the problem.
@GiovanniBussi GiovanniBussi changed the title But in masses passed to namd Bug in masses passed to namd Jul 16, 2015
@GiovanniBussi
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As discussed here it is possible to avoid re-patching and re-compiling namd just by adding in the input file something like
DUMPATOMS ATOMS=1-10000 STRIDE=5000000 FILE=test.xyz
Here 10000 is the number of atoms of the system and 500000 is larger than the number of simulation steps.
This however does not fix the problem on charges.

GiovanniBussi added a commit that referenced this issue Feb 17, 2016
@GiovanniBussi
Added a check that masses/charges are actually passed from MD
29739c5 
This is related to the closed issue #162

I think that with standard usage of PLUMED all the actions should be
active at step zero, and so all the masses and charges should be requested
to codes like NAMD or OPENMM. Anyway,this fix will double check for it
adding an overhead only at the first simulation step.
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