Bug #808
vsites and couple-lambda0 incompatibility?
Description
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 http://www.gromacs.org/Documentation/Errors
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
History
#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.