Do we need to process trajectory before sasa calculations?

User discussions
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1

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.

2

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

3

I think it looks suspicious. Could you post your annealing mdp settings?

4

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

5

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.

6

Thank you very much for your clarification.