Project

General

Profile

Bug #1749

pairs_nb is unknown directive in grompp

Added by Mark Abraham about 2 years ago. Updated about 2 years ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
Probably all since 4.0
Affected version:
Difficulty:
uncategorized
Close

Description

9a9ec966a50f69c6f035ccd36fb6b646c019848d moved [pairs] type 3 to [pairs_nb] but didn't add a case statement for parsing the new directive when found in a [moleculetype] entry.

Reported on gmx-users by Joao Martins

Associated revisions

Revision 6887b524 (diff)
Added by Mark Abraham about 2 years ago

Fix pairs_nb not recognized as part of moleculetype

Old code gives "unknown directive" error from the default of the
switch statement.

Fixes #1749

Change-Id: I54977f76f82cfdbfd4a7070129aa365d4fe5e188

History

#1 Updated by Gerrit Code Review Bot about 2 years ago

Gerrit received a related patchset '1' for Issue #1749.
Uploader: Mark Abraham ()
Change-Id: I54977f76f82cfdbfd4a7070129aa365d4fe5e188
Gerrit URL: https://gerrit.gromacs.org/4666

#2 Updated by Mark Abraham about 2 years ago

In email to me, Joao reported

I've finished the testing, good results all around. I decided to test on ethane, since it's parametrized on charmm36 and this way I'd be able to test the pairs directives. This is a alchemistry modification using a modified version of the alchemistry website tutorial, my free energy mdp portion was as follows, with the difference being that the starred options were removed for testing pairs_nb:

free-energy              = yes
*couple-intramol          = no*
*couple-moltype           = Other_chain_X*
*couple-lambda0           = vdw-q*
*couple-lambda1           = none*
sc-alpha                 = 0.5
sc-power                 = 1
sc-sigma                 = 0.3
init-lambda-state        = X
coul-lambdas             = 0.0 0.05 0.10 0.20 0.35 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0
vdw-lambdas              = 0.0 0.00 0.00 0.00 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0
nstdhdl                  = 20
calc-lambda-neighbors    = -1 

When using the commands no modification was made on topology; for pairs_nb testing this was in my topology:

[ atomtypes ]
dHCA3A  HCA3A   0.0000  0.000    A      0.000   0.000
dCC33A  CC33A   0.0000  0.000    A      0.000   0.000

[ moleculetype ]
; Name            nrexcl
Other_chain_X       3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
; residue   1 ETHA rtp ETHA q  0.0
     1      HCA3A      1   ETHA    H11      1       0.09      1.008  dHCA3A    0.000       1.008  ; qtot 0.09
     2      HCA3A      1   ETHA    H12      2       0.09      1.008  dHCA3A    0.000       1.008  ; qtot 0.18
     3      HCA3A      1   ETHA    H13      3       0.09      1.008  dHCA3A    0.000       1.008  ; qtot 0.27
     4      CC33A      1   ETHA     C1      4      -0.27     12.011  dCC33A    0.000      12.011  ; qtot 0
     5      HCA3A      1   ETHA    H21      5       0.09      1.008  dHCA3A    0.000       1.008  ; qtot 0.09
     6      HCA3A      1   ETHA    H22      6       0.09      1.008  dHCA3A    0.000       1.008  ; qtot 0.18
     7      HCA3A      1   ETHA    H23      7       0.09      1.008  dHCA3A    0.000       1.008  ; qtot 0.27
     8      CC33A      1   ETHA     C2      8      -0.27     12.011  dCC33A    0.000      12.011  ; qtot 0

...

[ pairs_nb ]
;  ai    aj funct            c0            c1            c2            c3
    1     5     1  0.09 0.09 0.238760856 0.10042
    1     6     1  0.09 0.09 0.238760856 0.10042
    1     7     1  0.09 0.09 0.238760856 0.10042
    2     5     1  0.09 0.09 0.238760856 0.10042
    2     6     1  0.09 0.09 0.238760856 0.10042
    2     7     1  0.09 0.09 0.238760856 0.10042
    3     5     1  0.09 0.09 0.238760856 0.10042
    3     6     1  0.09 0.09 0.238760856 0.10042
    3     7     1  0.09 0.09 0.238760856 0.10042

...

The results I got were these:

Experimental: 1.8 +- 2.1
Pairs_nb : 2.302 +- 0.03
couple commands: 2.230 +- 0.03

This seems pretty good evidence that the re-enabled code path does what you'd think it did.

#3 Updated by Erik Lindahl about 2 years ago

  • Status changed from New to Fix uploaded

#4 Updated by Erik Lindahl about 2 years ago

  • Status changed from Fix uploaded to Resolved

#5 Updated by Erik Lindahl about 2 years ago

  • Status changed from Resolved to Closed

Also available in: Atom PDF