sobereva 发表于 2024-5-13 22:25
verlet情况的bug所致（在我来看是bug），之前论坛里我就回答过类似问题

谢谢老师解答

zhangfaxue 发表于 2024-5-13 21:29
老师还有一个问题需要请教，我的A为带COOH的分子，B为阳离子，他们的库伦相互作用我理解应该是负的表现为 ...

verlet情况的bug所致（在我来看是bug），之前论坛里我就回答过类似问题

zhangfaxue 发表于 2024-5-13 21:12
老师我用cutoff-scheme = group，提示Fatal error:rcoulomb must not be greater than rlist (twin-range ...

把rlist设成和rcoulomb/rvdw相同的值

sobereva 发表于 2024-5-10 23:43
用cutoff-scheme = group

老师还有一个问题需要请教，我的A为带COOH的分子，B为阳离子，他们的库伦相互作用我理解应该是负的表现为吸引力，但是为什么我算出来是正，是我renrun.mdp文件设置有问题还是和什么相关？

sobereva 发表于 2024-5-10 23:43
用cutoff-scheme = group

老师我用cutoff-scheme = group，提示Fatal error:rcoulomb must not be greater than rlist (twin-range schemes are not supported)
然后逐渐减小rcoulomb和rvdw直到rcoulomb=0.8，rvdw=0.8(都小于1）提示
NOTE 1 【file rerun2.mdp]:The group cutoff scheme is deprecated since GRoMAcs 5.0 and will beremoved in a future release when all interaction forms are supported forthe verlet scheme. The verlet scheme already scales better, and it iscompatible with GPUs and other accelerators
NOTE 2 file rerun2.mdp]:
For a correct single-point energy evaluation with nsteps = 0, usecontinuation =yes to avoid constraining the input coordinates.
ERROR 1 [file rerun2.mdp]:With coulombtype = Cut-off, rcoulomb should be >= rlist unless you use apotential modifier
ERROR 2lfile rerun2.mdp]:With vdwtype = cut-off, rvdw must be >= rlist unless you use a potentialmodifier
NOTE 3 「file rerun2.mdp]:You are using a cut-off for Vdw interactions with NVE, for good energyconservation usevdwtype=shift(possibly with Dispcorr)
NOTE 4 [file rerun2.mdp]:You are using a cut-off for electrostatics with NVE, for good energyconservation use coulombtype=PME-Switch or Reaction-Field-zero
求助老师使用cutoff-scheme = group应该怎么确定rvdw和rcoulomb

用cutoff-scheme = group