[gmx-users] dt in mdp

[Justin Lemkul]

On 4/10/20 4:17 PM, Alex wrote:
> On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul <jalemkul at vt.edu> 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 <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.
> By constraining all the bonds  "constraints = all-bonds", the simulation
> crashes in the first step immediately irrespective to the starting point of
> simulation, even if I continue the old working simulation.

Now we're getting somewhere. That suggests that at least one bond has 
deviated substantially from its equilibrium length, such that the 
constraint algorithm fails immediately. This also likely underlies the 
original failure - forces are building up on some atoms such that mdrun 
crashes.

You have either a bad geometry, inadequate topology, or both. Inspect 
the molecule(s) that mdrun complains about to see if the molecules are 
distorted by computing bond lengths and comparing against the force 
field's parameters.

It may be beneficial to re-minimize and equilibrate with the proper 
constraint scheme after validating that the topology is of sufficient 
quality.

-Justin

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Justin A. Lemkul, Ph.D.
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