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

Jones de Andrade jdandrade at iq.ufrgs.br
Sun May 26 15:50:41 CEST 2019


Have you tried the packmol software?

Good luck,

Jones de Andrade
(jdandrade at iq.ufrgs.br)
Lattes: http://lattes.cnpq.br/6675936210583999
Orcid: https://orcid.org/0000-0003-3429-8119

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
>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
>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 
>(http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation). I 
>wonder if anything has changed...
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