Bug #808

vsites and couple-lambda0 incompatibility?

Added by Peter Kasson over 9 years ago. Updated over 9 years ago.

preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
Affected version:


I'm getting a grompp error when I try to use the couple-lambda0
option in conjunction with vsites:
Source code file: /home/kasson/gromacs-4.5/src/kernel/vsite_parm.c, line: 392

Fatal error:
calc_vsite3_param not implemented for the general case (atom 3)
For more information and tips for troubleshooting, please check the GROMACS
website at

I think it's coming in toppush.c when we do:

static void decouple_atoms(t_atoms *atoms,int atomtype_decouple,
int couple_lam0,int couple_lam1) {
int i;

for(i=0; i<atoms->nr; i++) {
if (couple_lam0 ecouplamNONE || couple_lam0 ecouplamVDW) {
atoms->atom[i].q = 0.0;
if (couple_lam0 ecouplamNONE || couple_lam0 ecouplamQ) {
atoms->atom[i].type = atomtype_decouple;
if (couple_lam1 ecouplamNONE || couple_lam1 ecouplamVDW) {
atoms->atom[i].qB = 0.0;
if (couple_lam1 ecouplamNONE || couple_lam1 ecouplamQ) {
atoms->atom[i].typeB = atomtype_decouple;

I tried checking for ptype == eptVSite, but I'm not sure that's set yet.

1. can you think of a better way to fix this?
2. is there some other indicator of a virtual site that's set by
this point in the code?

BTW I'm not trying to do quantitative free energy calculations with
virtual sites

example.tgz (344 KB) example.tgz trivial example Peter Kasson, 09/09/2011 08:29 PM


#1 Updated by Peter Kasson over 9 years ago

PS grompp syntax was:
/usr/local/gromacs/bin/grompp -f fe.mdp -p topol -c solv -o test

#2 Updated by Peter Kasson over 9 years ago

  • Status changed from New to 3
  • % Done changed from 0 to 100

#3 Updated by Berk Hess over 9 years ago

Commit 6978b2fe9a1b09beac954e750b7a3b84f4ccee3d addresses this.
Can we close this issue?

#4 Updated by Peter Kasson over 9 years ago

  • Status changed from 3 to Closed

Yes. What is our policy/distinction between "Resolved" and "Closed?"

#5 Updated by Rossen Apostolov over 9 years ago

Typically a developer would "Resolve" an issue, then the project leader would go over it and if happy "Close" it. But since we don't really have this system we can remove "Resolved".

If you prefer we can leave "Resolved" instead, I don't have a strong feeling about it.

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