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标题: 求助：模拟退火时索引文件里设置组报错提示不是能量组 [打印本页]

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Author: 1121571266 时间: 2023-7-20 19:59
标题: 求助：模拟退火时索引文件里设置组报错提示不是能量组
在使用Gromacs进行模拟退火时，先由make ndx命令生成了索引文件，里面的[ SOL ]包含了所有的溶剂分子即水分子，在进行模拟退火时设置energygrp-excl = SOL SOL，运行grompp时报错提示SOL不是能量组，恳请各位大神帮助下这到底是怎么回事？难道Gromacs的能量组不是通过索引文件定义的吗？

以下是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
annealing = perodic no
annealing-npoints = 5 0
annealing-time =  0 5 10 15 20
annealing_temp = 300 400 500 600 700
tcoupl = v-rescale
tc-grps =C SOL
tau-t = 0.5 0.5
ref-t = 300 300
gen-vel = yes
gen-temp = 300
freezegrps = SOL
freezedim = Y Y Y
energygrp-excl = SOL SOL

以下是index.ndx文件（部分）：
[ SOL ]
  11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
  26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
  41 42 43 44 45 46 47 48 49 50 51 52 53 54 55
  56 57 58 59 60 61 62 63 64 65 66 67 68 69 70
  71 72 73 74 75 76 77 78 79 80 81 82 83 84 85

....后面的省略

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
srun: Job step aborted: Waiting up to 62 seconds for job step to finish.
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

Setting the LD random seed to -1343238409

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 -67159677

Velocities were taken from a Maxwell distribution at 300 K

Cleaning up constraints and constant bonded interactions with virtual sites
Warning: file does not end with a newline, last line:
1 2 3 4 5 6 7 8 9 10
Simulated annealing for group C: Periodic, 5 timepoints
Time (ps) Temperature (K)
   0.0    300.0
   5.0    400.0
   10.0    500.0
   15.0    600.0
   20.0    700.0

NOTE 1 [file grompp.mdp]:
  There is a temperature jump when your annealing loops back.

NOTE 2 [file grompp.mdp]:
  There are 3624 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 C is 27.00
Number of degrees of freedom in T-Coupling group SOL is 0.00

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

Fatal error:
SOL 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 4219702.0 ON m3cl1602 CANCELLED AT 2023-07-20T19:48:37 ***
srun: error: m3cl1602: task 0: Killed

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