Previous Thread
Next Thread
Print Thread
Joined: Aug 2009
Posts: 134
L
lqz Offline OP
Forum Member
OP Offline
Forum Member
L
Joined: Aug 2009
Posts: 134
Hi, all:

When I ran replica-exchange simulation with implicit solvent and GBSW model on a big molecule (with at least 200 residues) interacting with a small molecule, the simulation crashed with segmentation error with the following shown in the output file:

CHARMM> shake bonh param fast
SHKCOM> SHAKE parameters: TOL = 0.1000D-09 MXITer = 500

3611 constraints will held by SHAKE.
FSSHKINI: Fast shake initialized with 3611 bond constraints and 0 water constraints (3-center).
FSSHKINI: 1314 2-body (CH), 706 3-body(CH2), 295 4-body(CH3), 0 >4-body.
FSSHKINI: Fast shake initialized with 3611 bond constraints and 0 water constraints (3-center).
FSSHKINI: 3611 constraints are in groups of: 0
FSSHKINI: 1314 2-body (CH), 706 3-body(CH2), 295 4-body(CH3), 0 >4-body.

On the screen, it has the following error message:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7F79B58B3467
#1 0x7F79B58B3AAE
#2 0x7F79B4DBA66F
#3 0x6AA520 in __gbsw_MOD_db_surf1
#4 0x771756 in old_energy_
#5 0x607E1C in __energym_MOD_energy
#6 0x4E6F39 in dynamc_
#7 0x4D1AA4 in __dcntrl_mod_MOD_dcntrl
#8 0x4DE388 in __dcntrl_mod_MOD_dynopt
#9 0x415FEA in maincomx_
#10 0x417FAC in MAIN__ at charmm_main.F90:?
Segmentation fault

Even after I removed molsurf TRUE from the GBSW command line, it still showed the same error message. I am wondering where is the error.

Joined: Aug 2009
Posts: 134
L
lqz Offline OP
Forum Member
OP Offline
Forum Member
L
Joined: Aug 2009
Posts: 134
Could the reason be that the large molecule is too large, has 421 residues? The small protein only has 45 residues.

Joined: Aug 2009
Posts: 134
L
lqz Offline OP
Forum Member
OP Offline
Forum Member
L
Joined: Aug 2009
Posts: 134
The problem was solved by a small change in the initial structure.


Moderated by  BRBrooks, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.5
(Release build 20201027)
Responsive Width:

PHP: 7.3.31-1~deb10u1 Page Time: 0.008s Queries: 20 (0.005s) Memory: 0.7372 MB (Peak: 0.7819 MB) Data Comp: Off Server Time: 2022-09-28 00:03:20 UTC
Valid HTML 5 and Valid CSS