normal Reg: Collagen with explicit solvation

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11 years 7 months ago #1059 by gokulalgates
Reg: Collagen with explicit solvation was created by gokulalgates
dear all,
i am trying to run the collagen like peptide with explicit solvation (coarse graining model) but i am getting the following error

"starting mdrun 'Martini system from coll.pdb'
100000 steps, 3000.0 ps.

Step 1 Warning: pressure scaling more than 1%, mu: 1.01268 1.01268 1.01268 "

and it got killed


i am using the following mdp file

integrator = md
dt = 0.030
nsteps = 100000

nstlog = 1000
nstenergy = 500
nstxtcout = 500

nstlist = 10
ns_type = grid
pbc = xyz
periodic_molecules = no
rlist = 1.4

coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
epsilon_rf = 1
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2

tcoupl = V-rescale
tc-grps = system
tau_t = 1.0
ref_t = 298
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 6.0
compressibility = 3e-4
ref_p = 1.0


the same file was running for gas phase calculation of collagen

regards
singam

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11 years 7 months ago #1060 by djurre
Replied by djurre on topic Reg: Collagen with explicit solvation
The mdp file looks good. The pressure scaling error mostly indicates the system is not relaxed. Try to run a (longer) EM and a position restrained relaxation (possibly with a smaller time step first).

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