[gmx-users] dt in mdp

[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 <jalemkul at vt.edu> 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 bonds are fixed, so
>> your constraints should be "all-bonds" not "h-bonds."
>>
> Interesting, hopefully that is the problem.
>
>
>> I would also suggest you thoroughly validate the quality of the epoxy
>> molecule topology against QM data and bulk-phase properties, if possible.
>>
> As the ATB folks claim, the parameterization has been performed against a
> very high level DFT calculation, especially for the molecules with less
> than 50 atoms.
> I already have tested the density and it is in agreement with the
> experimental value.
>
> Regarding the "comm-grps = " , would you also please kindly let me know
> which one you would recommend for this system + plus a small single
> molecule called MOL_A which defuses from water inside the epoxy, specially
> for the PMF calculation of the Mol_A?
>   comm-grps = Other SOL     ;; (Other = thin_film and Mol_A)
> or
> comm-grps = system

I saw the conversation with David about this. I have nothing to add that 
he hasn't already said.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================