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标题: 请教关于gromacs运行报错Step 1 Pressure scaling more than 1%的问题 [打印本页]

作者
Author: jia1012428 时间: 2023-12-8 10:55
标题: 请教关于gromacs运行报错Step 1 Pressure scaling more than 1%的问题
老师，您好，我在我们实验室的超算上跑两个一样的任务，无论先跑哪一个都可以正常运行，当再跑第二个的时候，报错如下Step 1 Pressure scaling more than 1%. This may mean your system is not yet equilibrated. Use of Parrinello-Rahman pressure coupling during equilibration can lead to simulation instability, and is discouraged.
我的md.mdp文件如下
define =
integrator = md
dt       = 0.002 ; ps
nsteps    = 50000000 ;0.002*50000000=100000 ps=100 ns
comm-grps  = protein_pmp_lig
comm-mode  = angular
energygrps =
;
nstxout = 0
nstvout = 0
nstfout = 0
nstlog  = 5000
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-grps  = system
;
pbc = xyz
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb    = 1.0
vdwtype    = cut-off
rvdw       = 1.0
DispCorr    = EnerPres
;
Tcoupl  = V-rescale
tau_t = 0.2 0.2
tc_grps = protein_pmp_lig Water_and_ions
ref_t = 318 318
;
Pcoupl    = parrinello-rahman
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
;
freezegrps  =
freezedim =
constraints = hbonds

老师，我不太理解，两个一样的任务，先跑第一个，第二个报错；先跑第二个，第一个报错
请老师只指点，谢谢！

作者
Author: sobereva 时间: 2023-12-8 11:23
分清楚提示和报错，完全是两码事

参考北京科音分子动力学与GROMACS培训班（http://www.keinsci.com/workshop/KGMX_content.html） ppt：
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