各位老师好，我在gmx 2022.6版本运行mdrun使用-v输出信息时，不太明白输出信息的含义。虽然公社中已有...
gmx mdrun -v -deffnm nvt Reading file nvt.tpr, VERSION 2023.3 (single precision)Changing nst...
mdrun-v -deffnmnvt 第九步:分析数据。我们需要计算CO2的扩散系数。首先,我们需要将周期性边界条件进行unfolding,因为粒子很有可能会跑到盒子外面去,所以运行路程需要累加。 指令为:trjconv-snvt.tpr-fnvt.xtc-onvt_noPBC.xtc-pbcmol-ur compact 其次,做一个index文件。 指令是:make_ndx-fnvt.gro-oindex.ndx...
Re: [gmx-users] Optimising mdrun Robert Cordina Re: [gmx-users] Optimising mdrun Kevin Boyd Re: [gmx-users] Optimising mdrun Robert Cordina [gmx-users] 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out Seketoulie Keretsu Re: [gmx-users] 1 particles ...
>> mdrun -deffnm npt >> >> >> >> >> >> So, I have three questions: >> >> 1. Is the starting structure bad? >> > > Probably. > > > 2. Did I change the vdwd radii by a lot (0.105 to 0.5) >> > > Yes. And you shouldn't use those artificial values for anything el...
(using vi or other file editors): nsteps = 50000 gen_vel = no grompp -f md.mdp -po -c fbp_pr.gro -p fbp.top -o md.tpr -v -nice 0 mdrun -s md.tpr -o md.trr -c fbp_md.gro -e md.edr -x md.xtc -g md.log -v -nice 0 12 Visualize the trajectory of prmd by VMD...
继续往下走，执行gmx mdrun -v -deffnm em，就会出现Fatal error，如图:但如果使用 (2)em.mdp：inte...
mdrun-v -deffnmnvt 第九步:分析数据。我们需要计算CO2的扩散系数。首先,我们需要将周期性边界条件进行unfolding,因为粒子很有可能会跑到盒子外面去,所以运行路程需要累加。 指令为:trjconv-snvt.tpr-fnvt.xtc-onvt_noPBC.xtc-pbcmol-ur compact 其次,做一个index文件。 指令是:make_ndx-fnvt.gro-oindex.ndx...
/var/spool/pbs/mom_priv/jobs/1869547.lionxj.rcc.psu.edu.SC<http://1869547.lionxj.rcc.psu.edu.SC>: line 14: 2359 Segmentationfault mdrun -deffnm npt So, I have three questions: 1. Is the starting structure bad? Probably. 2. Did I change the vdwd radii by a lot (0.105 to 0.5...
Segmentation fault mdrun -deffnm npt So, I have three questions: 1. Is the starting structure bad? 2. Did I change the vdwd radii by a lot (0.105 to 0.5) 3. What value of table extension should be used for 1-4 interaction ( ...