hi, I am trying to do a normal mode analysis on a protein.I tried to energy minimize the structure, but was not being able to bring the Fmax less than that of the order 1.00000e-03. Then I used the following ".mdp" file where I used the l-bfgs minimization method, using "cut-off" for electrostatics and Van der Waals interaction with rvdw and rcuolomb=0.
define = -DFLEXIBLE constraints = none integrator = l-bfgs tinit = 0 nsteps = 15000 nbfgscorr = 50 emtol = .001 emstep = 0.1 gen_vel = yes gen-temp = 300 nstcomm = 1 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 0 ; ns algorithm (simple or grid) ns-type = simple ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = no ; nblist cut-off rlist = 0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-Off rcoulomb-switch = 0 rcoulomb = 0 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0 The Fmax went down to Maximum force = 9.67927896882578e-07 on atom 3271, after doing the energy minimization with the above parameters twice. Then I used the same parameters, (while only changing the "integrator=nm") and did the normal mode analysis. The maximum force as calculated before the NMA was Maximum force: 9.67928e-07. Thus the Fmax as calculated at the end of the energy minimization and at the start of the NMA was the same. But while going through the gromacs manual and the user mailing list archives, I have seen that the it is suggested that the van der Waals and Coulomb interactions should be calculated as switched Coulomb & van der Waals interactions; cutoffs e.g. at 1.0 nm, switched from 0.8 nm (or shifted from 0 nm). rlist at 1.2 to 1.3 Changing the parameters in nm.mdp file gives the following message:Maximum force: 2.50866e+02 Maximum force probably not small enough to ensure that you are in anenergy well. Be aware that negative eigenvalues may occur when theresulting matrix is diagonalized. If I use these parameters in the energy minimization step the Fmax does not go down. Have I done the process correctly, or should I try again to reduce the Fmax in energy minimization step using switched cuolomb and van der waals interactions and then do NMA. Any suggestion will be of great help. Thanking You, Sarbani Chattopadhyay
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