# Temperature raise in Gromacs run **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters\ **Created:** [November 7, 2024, 11:32am UTC](https://gromacs.bioexcel.eu/t/temperature-raise-in-gromacs-run/10500 "2024-11-07T11:32:24Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Priscilla](https://avatars.discourse-cdn.com/v4/letter/p/5f9b8f/32.png) [@Priscilla](https://gromacs.bioexcel.eu/u/Priscilla)\ **Post date:** [November 7, 2024, 11:32am UTC](https://gromacs.bioexcel.eu/t/temperature-raise-in-gromacs-run/10500/1 "2024-11-07T11:32:24Z")
Hi, I want to raise the temperature of a Polystyrebe melt systen that has run for 1000ns in 500K to 800K.Below is the gro.mdp I used to raise temperature with Temperature ramp. I would like to know T ramp method is good to raise the T in a system or is there any other reommended ways to do that in gromacs? In below script I used 800K in ref\_t and gen\_t and alsoannealing T as 500 800 based on my understanding. Please advice. ; Time step in ps dt = 0.001 ; Number of steps to run nsteps = 1000000000 ; Remove center of mass motion every 100 steps comm-mode = Linear nstcomm = 100 ; Write positions and velocities to the trr file every 5000 steps ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 500000 nstvout = 500000 ; Write to the log and energy file every 5000 steps nstlog = 500000 nstenergy = 500000 ; Calculate energies every 100 steps nstcalcenergy = 100 ; Write positions to three decimal places to xtc file every 5000 steps nstxout-compressed = 500000 compressed-x-precision = 1000 ; Use the Verlet cutoff scheme with grid neighbor searching; you should basically always use this when you can (the only time you wouldn’t would be if you were using tabulated potentials, buckingham interactions, or energy group exclusions; see manual for more detail) cutoff-scheme = Verlet ns\_type = grid ; Periodic in all three dimensions pbc = xyz ; Minimum cutoffs in nm for neighbor list, electrostatics, and LJ interactions. mdrun will tune rcoulomb for improved performance. rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 ; Use the PME algorithm (an alternative to PPPM) (this is very likely the electrostatics algorithm you want to use) coulombtype = PME ; Smoothly shift vdw interactions to zero at the cutoff vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet ; GENERATE VELOCITIES FOR STARTUP RUN = gen-vel = yes gen-temp = 800 gen-seed = 173529 ; Use the v-rescale thermostat with a time constant of 0.1 ps and temperature of 600. V-rescale correctly samples the canonical distribution. Nose-hoover would be another good choice. tcoupl = V-rescale tc-grps = System tau\_t = 0.1 ref\_t = 800 ;Use when ramping temperature annealing = single;ramps a single time to the final T and remains constant at final T annealing-npoints = 2 ;number of reference points (match the number of temps, ie 300K to 550K would be 2, one for each temp) annealing-time = 0 1000 ;ramping time in ps - (1000 is 1 ns) annealing-temp = 500 800 ;start and stop temp ; Don’t use pressure coupling. For NPT this should be set. For equilibration, Berendsen is best since it is more stable. For production runs, Parrinello-Rahman is best since it samples the correct ensemble. pcoupl = no pcoupltype = Isotropic tau-p = 1 refcoord-scaling = No ; Use the LINCS algorithm to turn all bonds with hydrogen atoms into constraints. This allows a larger timestep. (can also use shake if needed, but lincs is faster) constraint\_algorithm = lincs constraints = H-bonds ; Do not generate initial velocities; rather this run is a continuation from a previous run. Alternately, set gen\_vel to yes and give it a temperature to sample the maxwell distribution at, and set continuation to no. ;gen\_vel = no ;continuation = yes ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r = 1 ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [November 7, 2024, 12:25pm UTC](https://gromacs.bioexcel.eu/t/temperature-raise-in-gromacs-run/10500/2 "2024-11-07T12:25:50Z")
With those settings you generate velocities at 800 K and then your annealing settings will make your thermostat set the temperature to 500 K and then you quickly (in 1 ns) scale up the temperature to 800 K again. Is that really what you want? Why not `gen-temp = 500` and `ref_t = 500` (`ref_t` does not really matter, but I find the intention easier to understand if it matches the temperature of the generated velocities)? You are running for 1000 ns, but you are heating the system from 500 K to 800 K over a period of 1 ns. With such a short annealing time, is there a reason why you are starting at 500 K at all? Why not start at 800 K? Or set `annealing-time` to, e.g., `0 100000` to increase the temperature for 100 ns. Why are you using such a low `tau-t`? I’d recommend 0.5 - 2 ps.