Hello Zhicheng,
Thanks for the extra information, I am glad it worked for you, too.
All the best,
Qinghua
On 06/23/2018 04:51 PM, Zuo, Zhicheng wrote:
> Hi Qinghua!
>
>
> As you expected, this solution works! Thanks so much!
>
>
> If the atomic number of the dummy atom is assigned as "-1" in Mg.lib, the atomic number appearing
>
> in the generated topology file would become "2". Actually, any integer other than "1" is OK.
>
> One note is that if the atomic number is set to be "0", the NUMEXTRA (number of extra points found in topology)
>
> at the top of the topology needs to be changed as the number of the atoms of type "EPW".
>
>
> Best,
>
> Zhicheng
>
> ________________________________
> From: Qinghua Liao <scorpio.liao.gmail.com>
> Sent: Thursday, June 21, 2018 3:42:22 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] AMBER18 pmemd.cuda running error for divalent metal ions represented using multisite (dummy) atom model with the 12-6-4 LJ potential
>
> Hello Zhicheng,
>
> Thanks for your interest in our work.
>
> In the topology file, the atomic number was set as 1 for the dummy atom, so
> the program treat all the dummy atoms as hydrogen atoms, though the vdW
> parameters are set ZERO.
>
> You can set the atomic number of the dummy atom as *-1* in the library
> file (*.lib). I think it can fix the problem.
> Please let me know if it works or not.
>
>
> All the best,
> Qinghua
>
> On 06/21/2018 11:45 PM, Zuo, Zhicheng wrote:
>> Hi,
>> The recently released AMBER18 adds GPU support for 12-6-4 ion potentials.
>> I did some tests, and found that it did works for the case where an ion is treated
>> traditionally as a single point charge with the 12-6-4 LJ potential. However, for the simulation
>> of the recent multisite ion (dummy atom) model with the 12-6-4 potential (https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpubs.acs.org%2Fdoi%2F10.1021%2Facs.jpclett.7b02358&data=01%7C01%7CZhicheng.Zuo%40unthsc.edu%7C6c0c10569258411f091808d5d7c84f29%7C70de199207c6480fa318a1afcba03983%7C0&sdata=Feb2BPyJ1B55nxFamU7RzR%2Bg%2Fb0vHKXtGYaXvX9l7BY%3D&reserved=0),
>> I got the following error from pmemd.cuda:
>> "Too many hydrogens for a hydrogen network, exiting."
>>
>> Interestingly, there is no any problem with the cpu version of pmemd for the 12-6-4 multisite ion model above.
>>
>> It seems that this issue is related to implementation of pmemd.cuda toward such a special divalent ion model.
>> Can someone help to figure it out? Thanks!
>>
>> Best,
>> Zhicheng Zuo
>> Postdoc research associate from College of Pharmacy,
>> UNT Health Science Center, Fort Worth, TX, USA.
>>
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Received on Tue Jun 26 2018 - 15:00:03 PDT
