Dear Researcher
I am having trouble during free energy calculation in gromacs as below:-
I ran an MD simulation for 3ns and from the last coordinates started a free energy calculation for 3ns. My system is well equilibrated but after 710725 steps I am getting Lincs warning every time as below:-
WARNING: There are no atom pairs for dispersion correction starting mdrun 'GROtesk MACabre and Sinister in water' 1500000 steps, 3000.0 ps.
Step 710726, time 1421.45 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000003, max 0.000023 (between atoms 5470 and 5472) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 43.8 0.1080 0.1080 0.1080
Step 710726, time 1421.45 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000003, max 0.000021 (between atoms 5470 and 5472) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 43.1 0.1080 0.1080 0.1080
I have added restraints between atoms of ligand and protein and getting Lincs warning between 1 atom included in restraints as below:-
[ bonds ] ; i j type r0A r1A r2A fcA r0B r1B r2B fcB 3437 7908 10 0.418 0.418 10.0 0.0 0.418 0.418 10.0 41840.00
[ angle_restraints ] ; ai aj ak al type thA fcA multA thB fcB multB 3437 7908 7906 7908 1 100.29 0.0 1 100.29 418.40 1 7908 3437 3439 3437 1 146.50 0.0 1 146.50 418.40 1
[ dihedral_restraints ] ; ai aj ak al type phiA dphiA fcA phiB dphiB fcB 7906 7908 3437 3439 1 156.16 0.0 0.0 156.16 0.0 418.40 7907 7906 7908 3437 1 -56.93 0.0 0.0 -56.93 0.0 418.40 7909 3437 3430 3435 1 131.32 0.0 0.0 131.32 0.0 418.40
Can anyone please suggest to me how Should I fix this error? I posted the question in the mailing list as well but didn't get any reply. Any help will be really appreciated.
Thanks.
Sadaf
Turn the LINCS option off and use a shorter time step in free energy calculation.
Zhaoxi Sun, thank you for your reply. Actually my system crashes and generates many pdb structures during which lincs warnings are generated. I also tried with 1 fs time step but still facing same problem. I am still unable to find any solution to the problem. What else should I do?
Thanks in advance.
Sadaf
Dear Zhaoxi Sun, I removed Lincs constraints and my system converged successfully when using a time step of 0.5 fs. I wonder is it the correct way because in literature I found people using constraints on h-bonds with a time step of 2 fs. I need your expert advice, please. Thanks
Dear Sadaf Rani I have the same problem as you. I can not define time steps more then 0.5 fs. When I use time step of 1 fs I face with lincs error between C-H bonds. But, when I use 0.5 fs time step it converges very good. How did you fix your problem?
Thank you
Dear Mohammad Rezayani I could not solve this problem yet. If anyone could please suggest a solution?
Thanks
Dear Sadaf Rani I could not find too. Somebody tell problem goes back to topology file. But, I checked it out many times.There were,actually, no problem in my topology file. If I find any solution I will tell you.
Thanks
Dear Sadaf Rani I could solve the problem. The main problem in my case was related to my topology file( itp file). As, I had to write my itp file by hand I had mistakes in my [bonds] part. I wrote bonds in two way wrongly. I mean for example I wrote:
[bonds]
14 15 1
15 14 1
while I must just write one of them. Because, it was repetitive and I faced with that warning. I hope it can help you .
Best
Dear Mohammad Rezayani thank you very much for your suggestion.
Could you please share a sample topology file?
Thanks.
Sadaf
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