Re: [gmx-users] dt in mdp

2020-04-10 Thread Justin Lemkul
On 4/10/20 4:17 PM, Alex wrote: On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote: On 4/10/20 9:16 AM, Alex wrote: Thank you for the response. On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: On 4/10/20 8:13 AM, Alex wrote: Dear Justin, Any comment please? Sorry, haven't had

Re: [gmx-users] dt in mdp

2020-04-10 Thread Alex
On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote: > > > On 4/10/20 9:16 AM, Alex wrote: > > Thank you for the response. > > > > > > On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: > > > >> > >> On 4/10/20 8:13 AM, Alex wrote: > >>> Dear Justin, > >>> Any comment please? > >> Sorry,

Re: [gmx-users] dt in mdp

2020-04-10 Thread Justin Lemkul
On 4/10/20 9:16 AM, Alex wrote: Thank you for the response. On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: On 4/10/20 8:13 AM, Alex wrote: Dear Justin, Any comment please? Sorry, haven't had power/network for a while due to some bad storms here. GROMOS force fields are

Re: [gmx-users] dt in mdp

2020-04-10 Thread Alex
Thank you for the response. On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: > > > On 4/10/20 8:13 AM, Alex wrote: > > Dear Justin, > > Any comment please? > > Sorry, haven't had power/network for a while due to some bad storms here. > > GROMOS force fields are parametrized assuming all

Re: [gmx-users] dt in mdp

2020-04-10 Thread Justin Lemkul
On 4/10/20 8:13 AM, Alex wrote: Dear Justin, Any comment please? Sorry, haven't had power/network for a while due to some bad storms here. GROMOS force fields are parametrized assuming all bonds are fixed, so your constraints should be "all-bonds" not "h-bonds." I would also suggest you

Re: [gmx-users] dt in mdp

2020-04-10 Thread Alex
Dear Justin, Any comment please? Regards, Alex On Tue, Apr 7, 2020 at 5:38 PM Alex wrote: > Thanks Justin for the response. > Please find below the mdp file. > The system is a thin film made out of a epoxy molecule, picture in be > below link, with water on top and bottom of the film. I even

Re: [gmx-users] dt in mdp

2020-04-07 Thread Alex
Thanks Justin for the response. Please find below the mdp file. The system is a thin film made out of a epoxy molecule, picture in be below link, with water on top and bottom of the film. I even sometimes have the same issue when I simulate the bulk of this system, I mean a cubic box filled by