[gmx-users] bad contacts on lipid tails

[Mohsen Ramezanpour]

I have done equilibration for almost 45 ns or even 60 ns for one test
system.

I expected with this energy and this equilibration time, it works fine. But
it fails.

I will construct the systems as you suggested to see what I get.

Thanks

On Wed, Jun 14, 2017 at 3:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/14/17 5:18 PM, Mohsen Ramezanpour wrote:
>
>> Hi Justin,
>>
>> Thanks for your reply,
>>
>> Here are the outputs for EM step:
>>
>> Steepest Descents converged to Fmax < 100 in 5198 steps
>> Potential Energy  = -2.6418572e+05
>> Maximum force     =  9.5666359e+01 on atom 54770
>> Norm of force     =  5.7127428e+00
>>
>> It seems okay to me.
>>
>> I chose the setting you mentioned.
>>
>> Interestingly, it also works for MD with dt=1 fs. Not for dt=2 fs, though.
>> Based on visualization, some lipid chains are crossed which I think this
>> cause the problem. Not sure how can I fix them.
>>
>>
> Surprising.  With such a low force, I wouldn't expect there to be any
> overlap or detrimental close contact.  An initial equilibration with dt = 1
> fs is a possibility, or a more robust method for constructing the system,
> whatever that may be.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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