# Langevin dynamics of protein in vacuum **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters\ **Created:** [May 7, 2024, 5:13pm UTC](https://gromacs.bioexcel.eu/t/langevin-dynamics-of-protein-in-vacuum/9098 "2024-05-07T17:13:02Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![acasavilca](https://avatars.discourse-cdn.com/v4/letter/a/bcef8e/32.png) [@acasavilca](https://gromacs.bioexcel.eu/u/acasavilca)\ **Post date:** [May 7, 2024, 5:13pm UTC](https://gromacs.bioexcel.eu/t/langevin-dynamics-of-protein-in-vacuum/9098/1 "2024-05-07T17:13:02Z")
GROMACS version: 2023-2 GROMACS modification: No Dear All, I am trying to implement Langevin dynamics for an in-vacuum protein system with PBC and large cutoffs for Coulomb and VdW interactions (no PME), and OPLS-AA as ff. I have two questions: 1. When using the recommended value tau\_t = 2 ps, which here defines the inverse friction constant, the recorded temperature (using gmx energy) stabilizes at ~265 K, while my set temperature (in mdp file) is 300K. I only made the recorded and set temperature match when lowering tau\_t to 0.2. Although I am still seeing the predicted behavior for my protein (compaction, about in a slower fashion), I am not sure about how to interpret the temperature change. In addition, I would expect tau\_t for an in-vacuum or gas phase system to be higher, as the inverse friction constant of water should be lower (higher friction constant). How could this be interpreted? 2. Using Langevin as both integrator and thermostat has been the only way I have got my vacuum and PBC protein system to work with a commonly used force field like OPLS. Using other integrators and thermostats have resulted in the system being very unstable, especially at high temperatures. Has Langevin dynamics been used for in-vacuum protein systems? I have not found published articles about this. Below is my nvt.mdp file with tau\_t = 0.2 ps: title = OPLSAA NVT equilibration ; Run parameters integrator = sd ; nsteps = 1000000 ; dt = 0.001 ; ; Mode for center of mass motion removal comm-mode = Linear ; remove center of mass ; Output control nstxout = 0 ; save coordinates every 1.0 ps nstvout = 0 ; save velocities every 1.0 ps nstfout = 0 ; nstvout, and nstfout nstenergy = 1000 ; save energies every 1.0 ps nstlog = 1000 ; update log file every 1.0 ps nstxout-compressed = 1000 ; save compressed coordinates every 1 ps (default 5000) compressed-x-grps = System ; save the whole system ; Bond parameters continuation = no ; first dynamics run constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs\_iter = 2 ; accuracy of LINCS lincs\_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns\_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rcoulomb = 333.3 ; short-range electrostatic cutoff (in nm) rvdw = 333.3 ; short-range van der Waals cutoff (in nm) DispCorr = no ; account for cut-off vdW scheme rlist = 333.3 ; short-range neighbour list cut-off ; Electrostatics coulombtype = cutoff ; Particle Mesh Ewald for long-range electrostatics pme\_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tc-grps = System ; two coupling groups - more accurate tau\_t = 0.2 ; time constant, in ps ref\_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen\_vel = yes ; assign velocities from Maxwell distribution gen\_temp = 300 ; temperature for Maxwell distribution gen\_seed = -1 ; generate a random seed ---
**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:** [May 22, 2024, 8:36am UTC](https://gromacs.bioexcel.eu/t/langevin-dynamics-of-protein-in-vacuum/9098/2 "2024-05-22T08:36:54Z")
I don’t see a reason for using Langevin Dynamics. Having said that, both LD and normal MD should not results in such large temperature deviations. I don’t see anything strange in your MD settings, so I have no clue what could be the cause of this. ---
**Author:** ![acasavilca](https://avatars.discourse-cdn.com/v4/letter/a/bcef8e/32.png) [@acasavilca](https://gromacs.bioexcel.eu/u/acasavilca)\ **Post date:** [May 22, 2024, 5:37pm UTC](https://gromacs.bioexcel.eu/t/langevin-dynamics-of-protein-in-vacuum/9098/3 "2024-05-22T17:37:35Z")
Thank you for your response. Could you expand on why there is no reason for using LD here?