Constraint error in algorithm Lincs at step 0 step 0 p0_30415: p4_error: interrupt SIGSEGV: ...
constraint_algorithm = lincs ; #约束算法 lincs :不能用于角度约束 constraints = all-bonds ; #键约束,all-bonds:所有键约束 lincs_iter = 1 ; #迭代次数,用于LINCS约束精度,默认1 lincs_order = 4 ; #约束偶合矩阵阶次,用于LINCS约束精度,默认4 ; Neighborsearching cutoff-scheme = Verlet ns_type = ...
=h-bonds; Type of constraint algorithmconstraint-algorithm = lincs; Do not constrain the start...
2 DispCorr = EnerPres ;constraints = none constraint_algorithm = LINCS implicit_solvent = no ...
constraint_algorithm = lincs ;Algorithm to restrict lincs_iter = 1 ;Number of iterations ...
integration algorithm (in |Gromacs| this is normally leap-frog), leapfrog). * Removalof centerof mass motion: when doing this in more than one group the conservation of will be violated. @@ -365,10 +367, @@ Other sources of possible problems are in the biomolecule topology itself...
All GROMACS optimizations were terminated once the maximum force became smaller than 0.004 kJ⋅mol-1⋅nm-1, using a conjugate gradient algorithm. A restraint force of 30 000 kcal⋅mol-1⋅rad-1 using AMBER’s NMR restraint option was used, while for GROMACS a dihedral_restraints section...
constraint-algorithm = Lincs ; Do not constrain the start configuration continuation = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 0.0001 ; Highest order in the expansion of the constraint coupling matrix ...
constraint-algorithm: 能够满足所有非 SETTLE 完整约束的求解算法。LINCS: 线性约束求解器(LINear Constraint Solver)。通过区域分解,使用并行版本的 P-LINCS。精度由 lincs-order 设置,该值设置了矩阵逆展开中的矩阵数。在矩阵求逆校正之后,该算法进行迭代校正,以补偿由于旋转引起的延长。这种迭代的次数可以用 lincs-...
yes ; Restarting after NPTconstraint_algorithm = lincs ; holonomic constraintsconstraints ...