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标题: 求助：设置用显卡加速PME计算 [打印本页]

作者
Author: botu 时间: 2022-3-8 13:49
标题: 求助：设置用显卡加速PME计算
本帖最后由 botu 于 2022-3-8 13:49 编辑

使用CHARMM-GUI生成的膜-蛋白输入文件，想在gmx mdrun命令中设置PME计算也用显卡加速，但是添加上-pme gpu之后，运行会报如下错误：
Feature not implemented:
Cannot compute PME interactions on a GPU, because PME GPU does not support not a dynamical integrator.

想请教一下这是漏安装了什么造成的还是。。？如果用 -bonded gpu的话会出现这种情况：
Inconsistency in user input:
Bonded interactions on the GPU were required, but not supported for these simulation settings. Change your settings, or do not require using GPUs.

(, 下载次数 Times of downloads: 19) (, 下载次数 Times of downloads: 16)
图1是README的内容，图2是报错
（非常感谢！）

作者
Author: 喵星大佬 时间: 2022-3-8 16:17
你在做能量极小化？
只有md支持pme gpu

作者
Author: sobereva 时间: 2022-3-8 22:10
把mdp贴出来

作者
Author: botu 时间: 2022-3-10 20:49

sobereva 发表于 2022-3-8 22:10
把mdp贴出来

老师好，谢谢回复！！  mdp如下：
1）step6.0_minimization.mdp
define                = -DPOSRES -DPOSRES_FC_BB=4000.0 -DPOSRES_FC_SC=2000.0 -DPOSRES_FC_LIPID=1000.0 -DDIHRES -DDIHRES_FC=1000.0
integrator             = steep
emtol                = 1000.0
nsteps                = 5000
nstlist                = 10
cutoff-scheme          = Verlet
rlist                = 1.2
vdwtype                = Cut-off
vdw-modifier          = Force-switch
rvdw_switch          = 1.0
rvdw                   = 1.2
coulombtype          = PME
rcoulomb             = 1.2
;
constraints          = h-bonds
constraint_algorithm = LINCS

2）step6.6_equilibration.mdp
define                = -DPOSRES -DPOSRES_FC_BB=50.0 -DPOSRES_FC_SC=0.0 -DPOSRES_FC_LIPID=0.0 -DDIHRES -DDIHRES_FC=0.0
integrator             = md
dt                   = 0.002
nsteps                = 250000
nstxtcout             = 5000
nstvout                = 5000
nstfout                = 5000
nstcalcenergy          = 100
nstenergy             = 1000
nstlog                = 1000
;
cutoff-scheme          = Verlet
nstlist                = 20
rlist                = 1.2
vdwtype                = Cut-off
vdw-modifier          = Force-switch
rvdw_switch          = 1.0
rvdw                   = 1.2
coulombtype          = PME
rcoulomb             = 1.2
;
tcoupl                = berendsen
tc_grps                = SOLU MEMB SOLV
tau_t                = 1.0 1.0 1.0
ref_t                = 294.15 294.15 294.15
;
pcoupl                = berendsen
pcoupltype             = semiisotropic
tau_p                = 5.0
compressibility       = 4.5e-5  4.5e-5
ref_p                = 1.0    1.0
refcoord_scaling       = com
;
constraints          = h-bonds
constraint_algorithm = LINCS
continuation          = yes
;
nstcomm                = 100
comm_mode             = linear
comm_grps             = SOLU_MEMB SOLV

3）step7_production.mdp
integrator             = md
dt                   = 0.002
nsteps                = 500000
nstxout                = 50000
nstvout                = 50000
nstfout                = 50000
nstcalcenergy          = 100
nstenergy             = 1000
nstlog                = 1000
;
cutoff-scheme          = Verlet
nstlist                = 20
rlist                = 1.2
vdwtype                = Cut-off
vdw-modifier          = Force-switch
rvdw_switch          = 1.0
rvdw                   = 1.2
coulombtype          = PME
rcoulomb             = 1.2
;
tcoupl                = Nose-Hoover
tc_grps                = SOLU MEMB SOLV
tau_t                = 1.0 1.0 1.0
ref_t                = 294.15 294.15 294.15
;
pcoupl                = Parrinello-Rahman
pcoupltype             = semiisotropic
tau_p                = 5.0
compressibility       = 4.5e-5  4.5e-5
ref_p                = 1.0    1.0
;
constraints          = h-bonds
constraint_algorithm = LINCS
continuation          = yes
;
nstcomm                = 100
comm_mode             = linear
comm_grps             = SOLU_MEMB SOLV

作者
Author: botu 时间: 2022-3-10 20:50

喵星大佬发表于 2022-3-8 16:17
你在做能量极小化？
只有md支持pme gpu

啊是的，极小化那一步就卡住了
（谢谢回复！）

作者
Author: botu 时间: 2022-3-12 20:42

喵星大佬发表于 2022-3-8 16:17
你在做能量极小化？
只有md支持pme gpu

是这一步不应该设置pme gpu……去掉之后后面就正常了

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