# Do we need to process trajectory before sasa calculations? **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools, gmx-sasa\ **Created:** [December 20, 2023, 10:37am UTC](https://gromacs.bioexcel.eu/t/do-we-need-to-process-trajectory-before-sasa-calculations/7896 "2023-12-20T10:37:52Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Ema2022](https://avatars.discourse-cdn.com/v4/letter/e/c5a1d2/32.png) [@Ema2022](https://gromacs.bioexcel.eu/u/Ema2022)\ **Post date:** [December 20, 2023, 10:37am UTC](https://gromacs.bioexcel.eu/t/do-we-need-to-process-trajectory-before-sasa-calculations/7896/1 "2023-12-20T10:37:52Z")
Dear All, I would like to know whether we need to use gmx trjconv -pbc nojump and get processed trajectory to be used in gmx sasa calculations OR can we use the trajectory straightway from the MD, without processing it with gmx trjconv? Thank you. ---
**Author:** ![Ema2022](https://avatars.discourse-cdn.com/v4/letter/e/c5a1d2/32.png) [@Ema2022](https://gromacs.bioexcel.eu/u/Ema2022)\ **Post date:** [January 4, 2024, 6:34pm UTC](https://gromacs.bioexcel.eu/t/do-we-need-to-process-trajectory-before-sasa-calculations/7896/2 "2024-01-04T18:34:43Z")
Dear All, I calculated SASA using the following command. The trajectory file (run.xtc) is not treated with gmx trjconv option. In my MD simulation, I followed two annealing cycles in each 50 ns simulation time. In the graph, I observed a pattern at every 25 ns and I am unable to explain why I get it. I would like to know whether I did any incorrect step in calculating SASA or whether this SASA behavior is normal in annealing. Appreciate your help on this. gmx sasa -s run.tpr -f .run.xtc -o sasa\_run.xvg -n index.ndx -tu ns ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/f/f9071939b69541cbf141c5de8608eb7ccc051510.png) ---
**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:** [January 9, 2024, 8:48am UTC](https://gromacs.bioexcel.eu/t/do-we-need-to-process-trajectory-before-sasa-calculations/7896/3 "2024-01-09T08:48:49Z")
I think it looks suspicious. Could you post your annealing mdp settings? ---
**Author:** ![Ema2022](https://avatars.discourse-cdn.com/v4/letter/e/c5a1d2/32.png) [@Ema2022](https://gromacs.bioexcel.eu/u/Ema2022)\ **Post date:** [January 9, 2024, 1:33pm UTC](https://gromacs.bioexcel.eu/t/do-we-need-to-process-trajectory-before-sasa-calculations/7896/4 "2024-01-09T13:33:29Z")
integrator = md nsteps = 50000000 ; two cycles of the annealing schedule below dt = 0.001 nstlist = 20 ns\_type = grid nstlog = 25000 nstenergy = 25000 nstxtcout = 25000 xtc\_precision = 25000 continuation = yes constraints = none lincs\_iter = 1 lincs\_order = 4 cutoff-scheme = Verlet rcoulomb = 1.4 rvdw = 1.4 coulombtype = PME pme\_order = 4 fourierspacing = 0.12 tcoupl = v-rescale tc-grps = System tau\_t = 0.100000 ref\_t = 310.0 nsttcouple = 5 pcoupl = Parrinello-Rahman pcoupltype = isotropic tau\_p = 1.000000 ref\_p = 1.000000 compressibility = 0.000045 nstpcouple = 1 refcoord\_scaling = com pbc = xyz DispCorr = EnerPres gen\_vel = no ; annealing schedule annealing = periodic annealing-npoints = 7 annealing-time = 0 1000 3000 13000 23000 24000 25000 annealing-temp = 310 325 360 360 360 325 310 ---
**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:** [January 12, 2024, 12:15pm UTC](https://gromacs.bioexcel.eu/t/do-we-need-to-process-trajectory-before-sasa-calculations/7896/5 "2024-01-12T12:15:52Z")
Sorry about the late reply, but I think it looks reasonable. What you see is a drop in SASA when the temperature drops from 360K to 310K. If you ran two shorter simulations (preferably starting from the end of the simulation that you presented above, as the equilibration time seems fairly long), one at 310K and one at 360K I think you would find a similar difference in SASA between them. ---
**Author:** ![Ema2022](https://avatars.discourse-cdn.com/v4/letter/e/c5a1d2/32.png) [@Ema2022](https://gromacs.bioexcel.eu/u/Ema2022)\ **Post date:** [January 16, 2024, 11:29am UTC](https://gromacs.bioexcel.eu/t/do-we-need-to-process-trajectory-before-sasa-calculations/7896/6 "2024-01-16T11:29:32Z")
Thank you very much for your clarification.