Hi
I am using gromacs 2020.2. I want to build a setup like in the figure attached here:
First I equilibrate a box of polymer/ion/water (in the middle of the box and blue area) and then added two water boxes on both sides of the relaxed polymer box (blue region) and finally justified box size based on the system size. The simulation procedure is successful in minimization. But, on nvt level I face to this error:
Step 3, time 0.003 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 4667552256.000000, max 644798283776.000000 (between atoms 6824 and 6829)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
81 85 90.0 0.1080 0.1860 0.1080
89 94 90.0 1.7146 1.8413 0.1080
92 97 51.2 38.5901 145.6929 0.1080
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
I changed the time step and checked the topology file tens of times but the error still remained. What is the main problem?
Thanks in advance
What was the outcome of energy minimization in terms of Fmax and Epot? If your first MD after minimization fails after 3 steps with such insane values, it wasn’t stable to begin with.
Dear Lemkul
I found the reason. My system size was very large. I decreased the number of water molecules and the problem is fixed.
Thank you
As you said that system size was very large and you decreased the number of water molecules. I have made a membrane complex with protein in Charmm gui and during running of energy minimization in Gromacs(2019.4 version) I’m getting this same an error of Segment fault(core dumped). My system ran upto step 87 and stops. It’s giving an error message segmentation fault(core dumped). But now whole system of ions, water was already made. How I will resolve this error? Kindly help me @mj.rezayani @jalemkul .
Hi Shivani,
This problem arises from different issues. Time step, topology file or system size. please double-check the .itp and .mdp file. you can use already made .mdp files in different websites like: (Lysozyme in Water). Also, decrease the time step for the first equilibration run. Moreover, you must avoid any molecule overlap while you set the simulation box.
Best,
Mohammad
Ok thank you for your suggestion. I will surely try to implement it.
