> Dear Servaas, > > In tleap did you really did: > > TLEAP > tleap -f leaprc.ff99SB > ad = sequence { DA5 DA DA3 } > saveamberparm da da_amber.top da_amber.crd > > > If so, it's wrong, it should be: > > saveamberparm ad da_amber.top da_amber.crd > ^^^ > and not 'da' Yes of course just a typo here > > Besides, I tried to reproduce what you did using what I think would be > fine and... everything went fine! Energies after minimisation in > single and double were almost identical and trajectories diverted > normally. Did you also try running it in vacuum? In solvent the problems occur only after a large number of steps. In vacuum they occur very fast. I know vacuum is not the way to go, but I consider it as quick test, if a short simulation in vacuum gives strange things it is an indication of a problem with the parameters (force fiels or others...). Amber doesn't give me any problems in vacuum, this gives me an indication that the vacuum is not the problem here. > > Please check what I did. > > # begin commands > > cat << EOF >| em.mdp > define = -DFLEXIBLE > integrator = cg ; steep > nsteps = 200 > constraints = none > emtol = 1000.0 > nstcgsteep = 10 ; do a steep every 10 steps of cg > emstep = 0.01 ; used with steep > nstcomm = 1 > coulombtype = PME > ns_type = grid > rlist = 1.0 > rcoulomb = 1.0 > rvdw = 1.4 > Tcoupl = no > Pcoupl = no > gen_vel = no > nstxout = 0 ; write coords every # step > optimize_fft = yes > EOF > > > cat << EOF >| md.mdp > integrator = md > nsteps = 1000 > dt = 0.002 > constraints = all-bonds > nstcomm = 1 > ns_type = grid > rlist = 1.2 > rcoulomb = 1.1 > rvdw = 1.0 > vdwtype = shift > rvdw-switch = 0.9 > coulombtype = PME-Switch > Tcoupl = v-rescale > tau_t = 0.1 0.1 > tc-grps = protein non-protein > ref_t = 300 300 > Pcoupl = parrinello-rahman > Pcoupltype = isotropic > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > gen_vel = yes > nstxout = 2 ; write coords every # step > lincs-iter = 2 > DispCorr = EnerPres > optimize_fft = yes > EOF > > > cat << EOF >| leap.in > verbosity 1 > source leaprc.ff99SB > ad = sequence { DA5 DA DA3 } > solvatebox ad TIP3PBOX 10.0 > addions ad Na+ 5 > addions ad Cl- 3 > saveamberparm ad da_amber.top da_amber.crd > savepdb ad DA.pdb > quit > EOF > tleap -f leap.in >| leap.out > > acpypi -x da_amber.crd -p da_amber.top -d > > #Single precision > grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr > mdrun -v -deffnm em > > #Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 22 steps > #Potential Energy = -6.2280516e+04 > #Maximum force = 7.5868494e+02 on atom 98 > #Norm of force = 1.0447179e+02 > > grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr > mdrun -v -deffnm md > > #Double precision > grompp_d -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr > mdrun_d -v -deffnm em > > #Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 22 steps > #Potential Energy = -6.22813514022256e+04 > #Maximum force = 7.58238100790309e+02 on atom 98 > #Norm of force = 1.04358667410458e+02 > > grompp_d -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr > mdrun_d -v -deffnm md > > # end commands > > Regards, > > Alan
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