Lysozyme-benzene cg simulation -Linc error

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1

GROMACS version:
GROMACS modification: Yes/No
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Hi, Sir/Ma’am

I am getting many linc warning at equilibration step (after increasing nstep) .

I did minimization step three times. used emtol=100, and increased nsteps.
linc error didnt come after that during minimization step. but i got linc error again at equilibration step. I attached my files also for your reference.

lincerror-lysozyme
lincerror-lysozyme1861×1017 146 KB

equilibration_lincerror
equilibration_lincerror1920×1080 204 KB

eq.mdp (4.6 KB)
min.mdp (4.6 KB)
CG_benzene.gro.txt (861.3 KB)
CG.gro.txt (861.2 KB)
Ps-commandline.txt (1.1 KB)

Thank you in advance for help.

2

Hi,
In the eq.mdp it says (in the comments):

; Most simulations are numerically stable with dt=40 fs, 
; however better energy conservation is achieved using a 
; 20-30 fs timestep. 
; Time steps smaller than 20 fs are not required unless specifically stated in the itp file.

You are running with a 50 fs timestep. That is quite optimistic. I would suggest not going over 30 fs per step. When equilibrating (especially as a first equilibration stage) you might have to go even lower. Try a 10 fs timestep and see if it helps.

3

Thank you so much for your reply. I will try and let you know the outcome,sir.