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标题: 求助：Gromacs运行模拟退火时定义了索引文件但是报错说不是能量组 [打印本页]

作者
Author: 1121571266 时间: 2023-7-19 19:31
标题: 求助：Gromacs运行模拟退火时定义了索引文件但是报错说不是能量组
如题所示，我在运行Gromacs的模拟退火任务时（体系是Fe表面上一个有机分子），在index.ndx文件中自己定义所有的Fe原子为[ Fe ], 所有有机分子的原子为[ MO ]，mdp文件如下，然后运行grompp时报错说Fe不是能量组，求助各位大神这是怎么回事？Gromacs的能量组应该如何定义？

mdp文件如下：
integrator = md
dt = 0.001
nsteps = 100000
nstxout = 100
nstvout = 100
nstfout = 100
nstlog = 100
nstcalcenergy = 100
nstenergy = 100
cutoff-scheme = Verlet
pbc = xyz
periodic-molecules = yes
verlet-buffer-tolerance = 0.001
vdwtype = Cut-off
vdw-modifier = Potential-shift
rvdw = 1
coulombtype = Cut-off
rcoulomb = 1
fourierspacing = 0.12
tcoupl = v-rescale
tau-t = 0.5 0.5
tc-grps = MO Fe
ref-t = 100 500
gen-vel = yes
gen-temp = 100
annealing = perodic no
annealing-npoints = 5 0
annealing-time = 0 5 10 15 20
annealing-temp = 100 200 300 400 500
freezegrps = Fe
freezedim = Y Y Y
energygrp-excl = Fe Fe

报错提示如下：
         :-) GROMACS - gmx grompp, 2022.2 (double precision) (-:

Executable: /public1/home/sch0015/Gromacs/DOUBLE-mpi/install/bin/gmx_mpi_d
Data prefix:  /public1/home/sch0015/Gromacs/DOUBLE-mpi/install
Working dir:  /public1/home/sch0015/Gromacs/DOUBLE-mpi/jobs/tpr
Command line:
  gmx_mpi_d grompp -f grompp.mdp -n index.ndx -c Model.gro -p Model.top -o run.tpr

Setting the LD random seed to -268722212

Generated 36 of the 36 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5

Generated 36 of the 36 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'Model'

Setting gen_seed to -143427651

Velocities were taken from a Maxwell distribution at 100 K

NOTE 1 [file Model.top, line 14]:
  In moleculetype 'Model' 900 atoms are not bound by a potential or
  constraint to any other atom in the same moleculetype. Although
  technically this might not cause issues in a simulation, this often means
  that the user forgot to add a bond/potential/constraint or put multiple
  molecules in the same moleculetype definition by mistake. Run with -v to
  get information for each atom.

Simulated annealing for group MO: Periodic, 5 timepoints
Time (ps) Temperature (K)
   0.0    100.0
   5.0    200.0
   10.0    300.0
   15.0    400.0
   20.0    500.0

NOTE 2 [file grompp.mdp]:
  There is a temperature jump when your annealing loops back.

NOTE 3 [file grompp.mdp]:
  There are 900 atoms that are fully frozen and part of COMM removal
  group(s), removing these atoms from the COMM removal group(s)

Number of degrees of freedom in T-Coupling group MO is 72.00
Number of degrees of freedom in T-Coupling group Fe is 0.00

-------------------------------------------------------
Program:    gmx grompp, version 2022.2
Source file: src/gromacs/gmxpreprocess/readir.cpp (line 3555)

Fatal error:
TEM in energygrp-excl is not an energy group

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
slurmstepd: error: *** STEP 4197666.0 ON m3cn0201 CANCELLED AT 2023-07-19T19:31:15 ***
srun: Job step aborted: Waiting up to 62 seconds for job step to finish.
srun: error: m3cn0201: task 0: Killed

求各位大神帮助解答，感激不尽。。。

作者
Author: sobereva 时间: 2023-7-20 12:22
看报错提示解决TEM in energygrp-excl is not an energy group，当前说的是TEM，搞清楚指的是什么

作者
Author: 1121571266 时间: 2023-7-20 14:48

sobereva 发表于 2023-7-20 12:22
看报错提示解决TEM in energygrp-excl is not an energy group，当前说的是TEM，搞清楚指的是什么

不好意思，社长，我发错了，我后来定义了[ TEM ]，还是不行，不知道问题在哪，另外想问下就是默认的组和自己在索引文件中定义的组可以一起使用吗，比如我做质心牵引时在索引文件里定义了[ CA ]和 [ CB ]两个组，然后在mdp里写tc-grps = System，然后运行grompp命令时提示System这个组找不到。

作者
Author: 1121571266 时间: 2023-7-20 14:52

sobereva 发表于 2023-7-20 12:22
看报错提示解决TEM in energygrp-excl is not an energy group，当前说的是TEM，搞清楚指的是什么

这是索引文件：
[ CA ]
1
[ CB ]
2

这是mdp文件：
integrator = md
dt = 0.001
nsteps = 1000000
nstxout = 100
nstvout = 100
nstfout = 100
nstlog = 100
nstcalcenergy = 100
nstenergy = 100
cutoff-scheme = Verlet
pbc = xyz
periodic-molecules = yes
verlet-buffer-tolerance = 0.001
vdwtype = Cut-off
vdw-modifier = Potential-shift
rvdw = 1.2
coulombtype = Cut-off
rcoulomb = 1.2
fourierspacing = 0.12
tcoupl = nose-hoover
tc-grps = System
tau-t = 0.5
ref-t = 300
gen-vel = yes
gen-temp = 300
pull = yes
pull-ngroups = 2
pull-ncoords = 1
pull-group1-name = CA
pull-group2-name = CB
pull-coord1-type = umbrella
pull-coord1-geometry = distance
pull-coord1-groups = 1 2
pull-coord1-start = no
pull-coord1-init = 0.3
pull-coord1-rate = 0
pull-coord1-k = 7000

报错信息如下：
         :-) GROMACS - gmx grompp, 2022.2 (double precision) (-:

Executable: /public1/home/sch0015/Gromacs/DOUBLE-mpi/install/bin/gmx_mpi_d
Data prefix:  /public1/home/sch0015/Gromacs/DOUBLE-mpi/install
Working dir:  /public1/home/sch0015/Gromacs/DOUBLE-mpi/jobs/tpr
Command line:
  gmx_mpi_d grompp -f grompp.mdp -n index.ndx -c sol.gro -p Model.top -o run.tpr

NOTE 1 [file grompp.mdp]:
  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

Setting the LD random seed to 1773133786

Generated 15 of the 15 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5

Generated 15 of the 15 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'Model'

Excluding 2 bonded neighbours molecule type 'SOL'

Setting gen_seed to -400197

Velocities were taken from a Maxwell distribution at 300 K

Cleaning up constraints and constant bonded interactions with virtual sites

-------------------------------------------------------
Program:    gmx grompp, version 2022.2
Source file: src/gromacs/gmxpreprocess/readir.cpp (line 3077)

Fatal error:
Group System referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
slurmstepd: error: *** STEP 4213278.0 ON m3cl1701 CANCELLED AT 2023-07-20T14:51:51 ***
srun: Job step aborted: Waiting up to 62 seconds for job step to finish.
srun: error: m3cl1701: task 0: Killed

作者
Author: sobereva 时间: 2023-7-20 19:28

1121571266 发表于 2023-7-20 14:48
不好意思，社长，我发错了，我后来定义了[ TEM ]，还是不行，不知道问题在哪，另外想问下就是默认的组和 ...

显然可以出现在一起

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