Hi <br><br>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<br>
<br>free_energy = yes<br>init_lambda = 0.0<br>delta_lambda = 5.0e-8<br><br>the no. of steps of the simulation is <br><br>nsteps = 20000000<br>dt = 0.025<br><br>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). <br>
<br>I have tried the following to continue my simulation:<br><br>1. I used the same *itp file and a new .mdp file with <br><br>free_energy = yes<br>init_lambda = 1.0<br>delta_lambda = 0.0<br><br>gen_vel = 0 <br><br>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. <br>
<br>The run crashed with the following msg<br><br>----------------------------------------------------------------------------------------------------------------------------------------------<br>Step 20000022, time 500001 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>rms inf, max inf (between atoms 345 and 346)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 345 346 90.0 0.2700 inf 0.2700<br>
345 347 90.0 0.2700 inf 0.2700<br> 346 347 90.0 0.2700 inf 0.2700<br> 354 355 90.0 0.2650 inf 0.2650<br>----------------------------------------------------------------------------------------------------------------------------------------------<br>
<br>Note: atoms 345, 346 and 347 are particles that have been changed to a new type during the fep run.<br><br>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".<br>
<br>The run crashed with the following msg<br>----------------------------------------------------------------------------------------------------------------------------------------------<br>starting mdrun 'MSCL PROTEIN IN MEMBRANE, SOLVATED, WITH IONS'<br>
20000000 steps, 500000.0 ps.<br>step 0<br>step 100, remaining runtime: 0 s<br>step 200, remaining runtime: 0 s<br><br>Step 264, time 6.6 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 4.088986, max 75.397156 (between atoms 455 and 456)<br>
bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 464 465 49.1 0.2700 0.2669 0.2700<br> 464 466 49.4 0.2700 0.2829 0.2700<br> 455 456 90.0 0.2650 20.2452 0.2650<br>
<br>----------------------------------------------------------------------------------------------------------------------------------------------<br><br>I also tried to simply minimize the confout.gro (ie the structure after the fep run has finished) but get the following <br>
<br>Double precision normally gives you higher accuracy.<br>You might need to increase your constraint accuracy, or turn<br>off constraints alltogether (set constraints = none in mdp file)<br><br>writing lowest energy coordinates.<br>
<br>Steepest Descents converged to machine precision in 99 steps,<br>but did not reach the requested Fmax < 10.<br>Potential Energy = -1.0321324e+06<br>Maximum force = 4.4505771e+03 on atom 462<br>Norm of force = 3.2656403e+01<br>
<br><br>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.<br>
<br>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. <br><br>any ideas are appreciated <br>
<br>Thanks <br>-- <br>Evelyne Deplazes<br><br>PhD student <br>Theoretical Chemistry group<br>University of Western Australia <br><br>