[gmx-users] non-water solvent + gmx solvate

[Alex]

Hi Kevin,

I'm using 2018.2 -- had to roll 2019 back because it segfaults on a 
certain simulation setup (I posted earlier about that, got no 
responses). Kind of a disappointing situation... I guess I will use 
packmol or just script it with insert-molecules.

Alex

On 5/26/2019 8:31 AM, Kevin Boyd wrote:
> Hi,
>
> Which version are you using? As of 2019 gmx solvate should support nonwater solvents and topology updating.
>
> If it’s not working with 2019, can you open up an issue on redmine.gromacs.org and upload your use files? I can take a look.
>
> Thanks,
>
> Kevin
>
>> On May 26, 2019, at 9:44 AM, Jones de Andrade <jdandrade at iq.ufrgs.br> wrote:
>>
>> Hi.
>>
>> Have you tried the packmol software?
>>
>> Good luck,
>>
>> Jones
>> -- 
>> Jones de Andrade
>> (jdandrade at iq.ufrgs.br)
>> DFQ/IQ/UFRGS
>> Lattes: https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flattes.cnpq.br%2F6675936210583999&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cb79a61ececb94475e39808d6e1e12970%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636944754526095853&amp;sdata=qLNraqM5cQFxHg95JtMQXWyTmr%2F6IP1bPR0naIrMFeU%3D&amp;reserved=0
>> Orcid: https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F0000-0003-3429-8119&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cb79a61ececb94475e39808d6e1e12970%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636944754526095853&amp;sdata=Hn05p%2B3u3jGeoz%2FBFjySrjbkfv5Z2WB5e%2B%2B5xYemVvo%3D&amp;reserved=0
>>
>> Enviado pelo K-9 mail
>>
>> Em 26 de maio de 2019 04:22:58 BRT, Alex <nedomacho at gmail.com> escreveu:
>>> Hi all,
>>>
>>> I have a custom model for acetonitrile, which works fine when filling
>>> up
>>> a box using insert-molecules. When trying to use gmx solvate starting
>>> from a non-empty box, the utility displays a promising "Generating
>>> solvent configuration" and proceeds into nothingness with 100% CPU
>>> load.
>>> Trying a range of -radius and -scale values does not help. The reason
>>> for using solvate is of course the automatic topology update and not
>>> having to specify the number of solvent molecules.
>>>
>>> Is there any hope or should solvate be abandoned for non-water? Yes, I
>>> did google this, and didn't like what I found
>>> (https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FHow-tos%2FNon-Water_Solvation&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cb79a61ececb94475e39808d6e1e12970%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636944754526095853&amp;sdata=t%2BM5WPuqKTDG07%2FwlnFGHsthnvd1V%2FR1NvJd4qBHEiw%3D&amp;reserved=0). I
>>> wonder if anything has changed...
>>>
>>> Thanks,
>>>
>>> Alex
>>>
>>> -- 
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cb79a61ececb94475e39808d6e1e12970%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636944754526095853&amp;sdata=Ic2fc%2FYfwbfIXDrS15CnjK%2BTW6vLVKj%2FfISqKzQRdlw%3D&amp;reserved=0 before
>>> posting!
>>>
>>> * Can't post? Read https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cb79a61ececb94475e39808d6e1e12970%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636944754526095853&amp;sdata=xPNqvbn6kY3TAxsgoT17uGaKNDWsSbcEhAFO7%2B1o7Cg%3D&amp;reserved=0
>>>
>>> * For (un)subscribe requests visit
>>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cb79a61ececb94475e39808d6e1e12970%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636944754526095853&amp;sdata=LgR0nViuQ2hmdFvkoFWb6R%2BItvmIWbwn6RVg%2B0bp0FU%3D&amp;reserved=0 or
>>> send a mail to gmx-users-request at gromacs.org.
>> -- 
>> Gromacs Users mailing list
>>
>> * Please search the archive at https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cb79a61ececb94475e39808d6e1e12970%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636944754526095853&amp;sdata=Ic2fc%2FYfwbfIXDrS15CnjK%2BTW6vLVKj%2FfISqKzQRdlw%3D&amp;reserved=0 before posting!
>>
>> * Can't post? Read https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cb79a61ececb94475e39808d6e1e12970%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636944754526095853&amp;sdata=xPNqvbn6kY3TAxsgoT17uGaKNDWsSbcEhAFO7%2B1o7Cg%3D&amp;reserved=0
>>
>> * For (un)subscribe requests visit
>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cb79a61ececb94475e39808d6e1e12970%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636944754526105860&amp;sdata=IspWJIUPcy6u6FzHLG7fOFayVxdcNGv29huFsRag438%3D&amp;reserved=0 or send a mail to gmx-users-request at gromacs.org.