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Joined: Aug 2009
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lqz Offline OP
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Dear all:

After running charmm-gui to set up the protein in POPC lipid bilayer simulation, I tried to run step6.1 to 6.6 using charmm program. The simulation crashed in the step6.1 step with the error message shown on screen as below:

DYNA> 0 0.00000-309377.14609 70401.08091-379778.22700 313.30225
DYNA PROP> 148.58556-302570.18635 90675.61322 6806.95973 98788.96453
DYNA INTERN> 831.57356 151.56471 15.12084 460.21733 57.45859
DYNA CROSS> -16.21059 0.00000 0.00000 0.00000
DYNA EXTERN> 33838.61111-344986.98071 0.00000 0.00000 0.00000
DYNA IMAGES> -240.95902 -13622.76149 0.00000 0.00000 0.00000
DYNA EWALD> 5439.7484-1911367.3962 1848892.9947 0.0000 0.0000
DYNA CONSTR> 193.14721 2.28811 0.00000 0.00000 0.00000
DYNA MMFP> 573.35637 0.00000 0.00000 0.00000 0.00000
DYNA PRESS> 18762.0401 -84621.3498 -1172.3902 -1510.3781 1097314.2664
---------- --------- --------- --------- --------- ---------
EPHI: WARNING. bent improper torsion angle is

far from minimum for;
IPHI= 212 with deltaPHI= 87.4292 MIN= 0.0000 ATOMS: 6546 6545 6548 6547
EPHI: WARNING. bent improper torsion angle is

far from minimum for;
IPHI= 354 with deltaPHI=-136.2591 MIN= 0.0000 ATOMS:16060160591606216061
EIPHIFS: WARNING. dihedral 404 is almost linear.
derivatives may be affected for atoms:19410194091941219411
EPHI: WARNING. bent improper torsion angle is

far from minimum for;
IPHI= 461 with deltaPHI= 99.7818 MIN= 0.0000 ATOMS:23287232862328923288
***** Error in fsshakph_kernel3 *****
CDYNA> 0 0.00000-309377.14609 70401.08091-379778.22700 313.30225
DYNA PROP> 148.58556-302570.18635 90675.61322 6806.95973 98788.96453
DYNA INTERN> 831.57356 151.56471 15.12084 460.21733 57.45859
DYNA CROSS> -16.21059 0.00000 0.00000 0.00000
DYNA EXTERN> 33838.61111-344986.98071 0.00000 0.00000 0.00000
DYNA IMAGES> -240.95902 -13622.76149 0.00000 0.00000 0.00000
DYNA EWALD> 5439.7484-1911367.3962 1848892.9947 0.0000 0.0000
DYNA CONSTR> 193.14721 2.28811 0.00000 0.00000 0.00000
DYNA MMFP> 573.35637 0.00000 0.00000 0.00000 0.00000
DYNA PRESS> 18762.0401 -84621.3498 -1172.3902 -1510.3781 1097314.2664
---------- --------- --------- --------- --------- ---------
EPHI: WARNING. bent improper torsion angle is

far from minimum for;
IPHI= 212 with deltaPHI= 87.4292 MIN= 0.0000 ATOMS: 6546 6545 6548 6547
EPHI: WARNING. bent improper torsion angle is

far from minimum for;
IPHI= 354 with deltaPHI=-136.2591 MIN= 0.0000 ATOMS:16060160591606216061
EIPHIFS: WARNING. dihedral 404 is almost linear.
derivatives may be affected for atoms:19410194091941219411
EPHI: WARNING. bent improper torsion angle is

far from minimum for;
IPHI= 461 with deltaPHI= 99.7818 MIN= 0.0000 ATOMS:23287232862328923288
***** Error in fsshakph_kernel3 *****
Coordinate resetting was not accomplished within 500 steps BY FAST METHOD.

*** LEVEL -2 WARNING *** BOMLEV IS 0
BOMLEV HAS BEEN SATISFIED. TERMINATING.

oordinate resetting was not accomplished within 500 steps BY FAST METHOD.

*** LEVEL -2 WARNING *** BOMLEV IS 0
BOMLEV HAS BEEN SATISFIED. TERMINATING.



Can someone check the charmm-gui online settings and help fixing the problem? Thank you very much.

Joined: Sep 2003
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rmv Online Content
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That can happen if you don't adequately prepare (e.g. minimize) the protein structure prior to uploading it, esp. for larger systems.


Rick Venable
computational chemist

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Dear Iqz, did your problem solved? I am having kind of same problem. I have used CHARMM-GUI to set up NAMD input for protein in POPC. But my simulation is crashing in first equilibration step step6.1_equilibration.inp showing the error-

REASSIGNING VELOCITIES AT STEP 10000 TO 313.15 KELVIN.
colvars: Writing the state file "step6.1_equilibration.restart.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file "step6.1_equilibration.colvars.traj".
ERROR: Constraint failure in RATTLE algorithm for atom 5899!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.

Thanks


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