计算化学公社

 找回密码 Forget password
 注册 Register
Views: 1100|回复 Reply: 1
打印 Print 上一主题 Last thread 下一主题 Next thread

[GROMACS] 四点水模型是否支持update gpu?

[复制链接 Copy URL]

3

帖子

0

威望

67

eV
积分
70

Level 2 能力者

跳转到指定楼层 Go to specific reply
楼主
本帖最后由 elloit 于 2024-4-15 17:53 编辑

在用opc/tip4p水模型做蛋白质MD的时候,使用-update gpu遇到报错,
Inconsistency in user input:
Update task on the GPU was required,
but the following condition(s) were not satisfied:
Virtual sites are not supported.

我gromacs版本是2024.1,大概是现在还不支持Virtual sites放到GPU上update,
但是看手册上的介绍又很迷惑
To completely avoid communication for constraints and/or to have the update run on a GPU, the system needs to support so-called “update groups” (or no constraints at all). Update groups are supported when all atoms involved in coupled constraints are coupled directly to one central atom and consecutively ordered, not interdispersed with non-constrained atoms. An example is a compactly described methyl group. For atomistic force fields with constraints = h-bonds this means in practice that in the topology hydrogens come adjacent to their connected heavy atom. In addition, when virtual sites are present, the constructing atoms should all be constrained together and the virtual site and constructing atoms should be consecutive, but the order does not matter. The TIP4P water model is an example of this. Whether or not update groups are used is noted in the log file. When they cannot be used, the reason for disabling them is also noted.

举了个TIP4P的例子,看似能支持gpu update,但实际运行还是报错说虚拟点不支持,所以"TIP4P water model is an example"这个example指的是反例吗,意思是用TIP4P确实不能使用-update gpu吗?

19

帖子

0

威望

133

eV
积分
152

Level 3 能力者

2#
发表于 Post on 2024-5-14 14:54:45 | 只看该作者 Only view this author
我用的是SOB老师编译的2020.6-WINDOWS-GPU版本,可以四点水模型结合UPDATE GPU

本版积分规则 Credits rule

手机版 Mobile version|北京科音自然科学研究中心 Beijing Kein Research Center for Natural Sciences|京公网安备 11010502035419号|计算化学公社 — 北京科音旗下高水平计算化学交流论坛 ( 京ICP备14038949号-1 )|网站地图

GMT+8, 2026-2-24 03:42 , Processed in 0.164686 second(s), 26 queries , Gzip On.

快速回复 返回顶部 返回列表 Return to list