# BD stops after some steps **URL:** \ **Category:** User discussions\ **Created:** [October 6, 2020, 3:54pm UTC](https://gromacs.bioexcel.eu/t/bd-stops-after-some-steps/918 "2020-10-06T15:54:29Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![cintia.vequi](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cintia.vequi/32/374_2.png) [@cintia.vequi](https://gromacs.bioexcel.eu/u/cintia.vequi)\ **Post date:** [October 6, 2020, 3:54pm UTC](https://gromacs.bioexcel.eu/t/bd-stops-after-some-steps/918/1 "2020-10-06T15:54:30Z")
GROMACS version: 2020.3 GROMACS modification: No I am performing Brownian Dynamics with hard spheres. But the simulation stops after a random number of steps, Gromacs keeps running but I don’t have evolution on the number of steps in any output file. First I was using only the C12 part of the LJ potential and I thought this problem could be due to two particles getting to close together and the potential getting to big. So I added the C6 term, the problem took longer to appear, the simulation was able to run for a longer time, but it is still there. I am putting below the mdp file I am using, the itp for the particles and the topology. The system is 1000 particles in a box of 5 x 5 x 5 um3. Any help is greatly appreciated! Thank you so much! _ **mdp file** _\_ ld-seed = 55560 ; Use random seed ;################################# INTEGRATOR ################################## integrator = bd ; Langevin thermostat dt = 1000 ; Timestep (ps) nsteps = 20000000 ; Simulation duration (timesteps) nstcomm = 0 ; Center of mass motion removal interval comm-mode = None ; Center of mass motion removal mode bd\_fric = 24000 ; The friction coefficient for each particle is calculated as mass/tau-t. ;################################## ENSEMBLE ################################### ref\_t = 295 ; System temperature (K) tau\_t = 2.0 ; Thermostat time constant (ps) tc\_grps = system ; Apply thermostat to complete system ;############################## IMPLICIT SOLVENT ############################### implicit\_solvent = no ; NO implicit solvent ;########################### NONBONDED INTERACTIONS ############################ cutoff\_scheme = Verlet ; Method of managing neighbor lists pbc = xyz ; Periodic Boundary Conditions in all directions coulombtype = cut-off ; Calculate coulomb interactions using PME rcoulomb = 10 ; Coulomb cutoff vdwtype = cut-off ; Calculate van der Waals interactions using PME rvdw = 10 ; Van der Waals cutoff rlist = 10 ; Neighbor list cutoff nstlist = 100 ; ;################################### OUTPUT #################################### nstlog = 5000 ; Log output interval (timesteps) nstenergy = 5000 ; Energy output interval (timesteps) nstcalcenergy = 5000 ; Energy calculation interval (timesteps) nstxout = 1000 ; Trajectory output interval (timesteps) nstvout = 5000 ; Velocity outout interval (timesteps) nstfout = 5000 ; Force output interval (timesteps) nstxout-compressed = 0 ; _ **itp file** _\_\_\_\_\_\_\_\_\_ ; Topology of solid particles. ; No include forcefield parameters [defaults] ; nb-type combination-rule gen-pairs fudgeLJ fudgeQQ 1 1 no [atomtypes] ;type mass charge ptype c6 c12 FA 4.8e+04 0.000 A 3.898e+04 6.090e+08 FB 3.0e+08 0.000 A 2.494e+12 2.494e+24 FC 1.03e+3 0.000 A 1.818e+03 1.326e+06 [nonbond\_params] FA FA 1 3.898e+04 6.090e+08 FB FB 1 2.494e+12 2.495e+24 FC FC 1 1.818e+03 1.326e+06 [moleculetype] ;name nrexcl F005 1 ; sigma=05nm Epsilon= 0.6236 kJmol-1 mass= 48000 Da C12= 6.08984e+08 kJmol-1nm12 [atoms] ; nr type resnr residu atom cgnr charge mass 1 FA 1 F005 FA 0 0.00 4.8e+04 [moleculetype] ;name nrexcl F100 1 ; sigma=100nm Epsilon= 0.6236 kJmol-1 mass= 3.0e+08 Da C12= 2.49440e+24 kJmol-1nm12 [atoms] ; nr type resnr residu atom cgnr charge mass 1 FB 1 F100 FB 0 0.00 3.0e+08 [moleculetype] ;name nrexcl F003 1 ; sigma=03nm Epsilon= 0.6236 kJmol-1 mass= 1029 Da C12= 1.32563e+06 kJmol-1nm12 [atoms] ; nr type resnr residu atom cgnr charge mass 1 FC 1 F003 FC 0 0.00 1.02914e+03 _ **top file** _\_\_\_ ; Topology of 1000 particles. #include “solidParticlesC6.itp” [system] ; systemname 1000 particles 005nm [molecules] ; molecule number F005 1000 ---
**Author:** ![cintia.vequi](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cintia.vequi/32/374_2.png) [@cintia.vequi](https://gromacs.bioexcel.eu/u/cintia.vequi)\ **Post date:** [October 7, 2020, 6:52am UTC](https://gromacs.bioexcel.eu/t/bd-stops-after-some-steps/918/2 "2020-10-07T06:52:51Z")
I forgot to say I generated the initial configuration with: gmx insert-molecules -ci 1particles5nm.gro -nmol 1000 -box 5000 5000 5000 -o 1000particles5nm.gro -radius 2.5 Thank again. ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [October 7, 2020, 11:31am UTC](https://gromacs.bioexcel.eu/t/bd-stops-after-some-steps/918/3 "2020-10-07T11:31:25Z")
It is a bit difficult to judge what the values of the parameters should be with your different than usual sizes and masses, but I think the timestep is many orders of magnitude too large. My guess is that atoms move thousands of box length and pbc corrections take forever. ---
**Author:** ![cintia.vequi](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cintia.vequi/32/374_2.png) [@cintia.vequi](https://gromacs.bioexcel.eu/u/cintia.vequi)\ **Post date:** [October 7, 2020, 1:01pm UTC](https://gromacs.bioexcel.eu/t/bd-stops-after-some-steps/918/4 "2020-10-07T13:01:12Z")
I get what you are saying but with BD ‘the system is assumed to be over-damped, large timesteps can be used’ as state in the Gromacs manual. So 1ns is too large? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [October 8, 2020, 8:16pm UTC](https://gromacs.bioexcel.eu/t/bd-stops-after-some-steps/918/5 "2020-10-08T20:16:22Z")
What is relevant for BD is dt/gamma, so one can’t speak about dt in isolation. But I would guess that 1 ns is several orders of magnitude too large. Try and see. ---
**Author:** ![cintia.vequi](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cintia.vequi/32/374_2.png) [@cintia.vequi](https://gromacs.bioexcel.eu/u/cintia.vequi)\ **Post date:** [October 9, 2020, 11:24am UTC](https://gromacs.bioexcel.eu/t/bd-stops-after-some-steps/918/6 "2020-10-09T11:24:07Z")
Thank you so much for your clarifications. I am learning a lot. I have dt/gamma around 1e-1. What would be reasonable values so I can adjust dt?? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [October 9, 2020, 11:44am UTC](https://gromacs.bioexcel.eu/t/bd-stops-after-some-steps/918/7 "2020-10-09T11:44:09Z")
If you read the manual, you see that the displacement in a step is force\*dt/gamma plus a random term. So you need to come up with a reasonable displacement and maximum force so you can estimate reasonable parameter values. The proper check is to see that you distribution of states is not affected by the time step. ---
**Author:** ![cintia.vequi](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cintia.vequi/32/374_2.png) [@cintia.vequi](https://gromacs.bioexcel.eu/u/cintia.vequi)\ **Post date:** [October 9, 2020, 1:18pm UTC](https://gromacs.bioexcel.eu/t/bd-stops-after-some-steps/918/8 "2020-10-09T13:18:40Z")
Thank you! I will do that.