Hi, I am trying to do normal mode analysis on a protein having 6398 atoms in vaccum.
I tried to energy minimize the structure using steepest descent, followed by "l-bfgs" minimization. the .mdp file I used is 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 after running the 15000 steps the Fmax was: Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 10197 steps Potential Energy = -8.26391832320506e+04 Maximum force = 9.37558560558845e-04 on atom 4562 Norm of force = 2.24887722104890e-04 Again the "l-bfgs" minimization was run using the same .mdp file( with emtol = 0.000001) the output was' Low-Memory BFGS Minimizer converged to Fmax < 1e-06 in 4143 steps Potential Energy = -8.26391832324998e+04 Maximum force = 9.67927896882578e-07 on atom 3271 Norm of force = 1.70637151528245e-07 After this I prepared the "nm.mdp " file for NMA, where I used exactly the same parameters as the ones used in lbfgs energy minimization( with integrator = nm) the commands that were used were: grompp_d -f new_nm.mdp -t new_lbfgs_2.trr -c new_lbfgs_2.gro -o new_nm.tpr -zero -p ../topol.top nohup mdrun_d -v -s new_nm.tpr -deffnm new_nm -mtx new_nm.mtx & "nohup.out" had the following message: Non-cutoff electrostatics used, forcing full Hessian format.Allocating Hessian memory...starting normal mode calculation 'Protein'6398 steps.Maximum force: 9.67928e- 07 The run ended successfully: Then i used the command g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr I get the following error: Reading file new_nm.tpr, VERSION 4.0.7 (double precision) Reading file new_nm.tpr, VERSION 4.0.7 (double precision) Reading double precision matrix generated by Gromacs VERSION 4.0.7 Full matrix storage format, nrow=19194, ncols=19194 Diagonalizing to find vectors 1 through 50... g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug I am not being able to understand the problem. the computer has a 16gb memory If I use different parameters in the nm.mdp file as rlist = 1.5 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = switch rcoulomb-switch = 1 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 1 rvdw = 1.2 then i get the message :Maximum force: 3.14171e+03 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. I am sorry to post such a lengthy query, but I have no clue about the root of the problem. Any suggestion will be of great help. Thanks in advance, Sarbani.
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