Hi I am simulating a system consisting of a protein embedded in membrane, solvated with water using the Martini forcefield. I have set up a free energy perturbation simulation where a subset of the protein particles are being converted from their original particle type (state A, lambda =0) to a new particle type (state B, lambda =1). I have finished a 500 ns run with the following fep options
free_energy = yes init_lambda = 0.0 delta_lambda = 5.0e-8 the no. of steps of the simulation is nsteps = 20000000 dt = 0.025 hence lambda = 1 after 500ns. so in theory the confout.gro should contain the structure with all the "fep" particles in state B. I now want to continue the simulation with the new particle types without any fep options (ie a simple md run). I have tried the following to continue my simulation: 1. I used the same *itp file and a new .mdp file with free_energy = yes init_lambda = 1.0 delta_lambda = 0.0 gen_vel = 0 I grommp-ed the new .mdp file (using the same *top, *itp and *gro file as for the original grompp) and continued the run using the state.cpt files from the end of the 500ns run. The run crashed with the following msg ---------------------------------------------------------------------------------------------------------------------------------------------- Step 20000022, time 500001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms inf, max inf (between atoms 345 and 346) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 345 346 90.0 0.2700 inf 0.2700 345 347 90.0 0.2700 inf 0.2700 346 347 90.0 0.2700 inf 0.2700 354 355 90.0 0.2650 inf 0.2650 ---------------------------------------------------------------------------------------------------------------------------------------------- Note: atoms 345, 346 and 347 are particles that have been changed to a new type during the fep run. 2. I made a new .itp file where I changed all the "fep" particles to be of the new type (ie state B) and removed all fep parameters in the .mdp file. I "re-grompped" with the confout.gro from the fep run and the new .itp and .mdp files. This should be like a new simulation without any "memory of its fep past". The run crashed with the following msg ---------------------------------------------------------------------------------------------------------------------------------------------- starting mdrun 'MSCL PROTEIN IN MEMBRANE, SOLVATED, WITH IONS' 20000000 steps, 500000.0 ps. step 0 step 100, remaining runtime: 0 s step 200, remaining runtime: 0 s Step 264, time 6.6 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 4.088986, max 75.397156 (between atoms 455 and 456) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 464 465 49.1 0.2700 0.2669 0.2700 464 466 49.4 0.2700 0.2829 0.2700 455 456 90.0 0.2650 20.2452 0.2650 ---------------------------------------------------------------------------------------------------------------------------------------------- I also tried to simply minimize the confout.gro (ie the structure after the fep run has finished) but get the following Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 99 steps, but did not reach the requested Fmax < 10. Potential Energy = -1.0321324e+06 Maximum force = 4.4505771e+03 on atom 462 Norm of force = 3.2656403e+01 I thought it might be that I am "re-grompping" and starting the simulation again. So I set up a test run where there is a continuous simulation. Total simulation time = 200ns and the fep options are set such that lambda reaches 1 after 100 ns. I was hoping the simulation would simply continue with the new particle type for the remaining 100 ns. But that crashed as well with similar LINCS warnings. Has anyone else ever had a similar problem? I have already spent a fair bit of time on trying to fix it and also talked to people from the Martini group who are experiences gromacs user. any ideas are appreciated Thanks -- Evelyne Deplazes PhD student Theoretical Chemistry group University of Western Australia
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