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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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