[gmx-users] bad contacts on lipid tails

[Mohsen Ramezanpour]

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.

Cheers,
Mohsen


On Wed, Jun 14, 2017 at 3:02 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/14/17 1:05 PM, Mohsen Ramezanpour wrote:
>
>> Dear Gromacs users,
>>
>> I am doing simulations in HII phase in absence of any sugar or alkane to
>> fill the gaps (in other words, HII in water)
>> In few of my systems (which I made), there are lipids which their tails
>> have bad contacts. Based on visualization, the CH2-CH2 bond from one tail
>> in lipid 1 cross the CH2-CH2 bond in the tail from an adjacent lipid. They
>> kinda stuck there.
>>
>> Interestingly, these systems are running properly during EM step, as well
>> as MD with a time step of 1 fs but fail with 2 fs, even after 45 ns of
>> simulation with 1 fs. The lipid-lipid contacts cause LINCS errors for
>> angles on those bonds and involved hydrogens, and eventually, the system
>> will blow up.
>>
>> This is what I understand after many tests to figure out the problem for
>> this failure (segmentation fault (core dumped)). The topology of the
>> molecule is correct and there is not water molecule which causes the
>> problem. I also did simulations on one lipid both in the vacuum and in
>> water. Everything is fine. The system setup is the only thing which I am
>> suspicious about.
>>
>> Is there any trick to:
>>
>> 1) recognize these bad contacts? (I deleted few lipids but still, there
>> are
>> other lipids which cause the problem)
>>
>>
> Nope, aside from your eyeballs and inspection of maximum forces following
> EM that might point to a problem.
>
> 2) remove these bad contacts? (applying stronger bond and angle force
>> constant, changing the LINCS parameters, or something like these?)
>>
>>
> Changing the force field is unwise.  Changing LINCS parameters can make
> the constraint algorithm more permissive and can overcome problems, but
> that can mask problems.
>
> If your system is crashing despite "successful" EM, that means you
> probably only found a metastable state.  One thing that we have recently
> found is that the default settings for the GROMACS steepest descent
> minimizer can lead to premature termination but a decrease of initial step
> size to e.g. 0.002 (instead of 0.01, which is the default) does a much
> better job, especially when we compare it to the CHARMM minimizer (which is
> pretty bulletproof and does a great job of resolving nasty clashes that
> GROMACS doesn't handle well with default settings).
>
> -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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