[gmx-users] Periodic Cell of Cyclohexane--LINCS Warnings

[Billy Williams-Noonan]

"Side issue, not related to your problem - use gmx grompp -t state.cpt to
get the full-precision coordinates and box."

I used gmx energy to plot the box coordinates over time.  Using P-R with a
2 fs timestep and tau_p of 2 ps, the box shrinks to a certain point, and
then the system "blows up".  This can also be visualised in VMD.  There is
no such problem when increasing tau_p to 6 ps.  Thanks, I think I know what
the problem is.

"At minimum, your use of rvdw = 1.0 is incorrect.  It should be 1.4.  This
could be related to instability of systems dominated by vdW interactions."

Thank you, will set rvdw to 1.4 nm.  I initially assumed 1.0 nm would be
fine, as that is how I read the mdp settings page for Gromacs*:*

rvdw (1) <http://manual.gromacs.org/online/mdp_opt.html#nl>

When I found out that my rvdw was wrong, I noticed that many people seem to
be using the wrong value for the cut-offs and still getting published.  I
understand that the varying force-fields were optimised under different
conditions.  My system appears to be stable now with the current
parameters, but I will fix to make the long-term energetics more correct
anyway.

Cheers for the help,

Billy

On 12 June 2017 at 21:54, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/12/17 6:25 AM, Billy Williams-Noonan wrote:
>
>> Thanks for your reply, Mark (Professor Abraham?)
>>
>> "Looks like some of the integration setups are more stable than others.
>> What
>> is the volume doing during these runs? What does P-R 2fs do after a stage
>> of P-R 1fs?"
>>
>> P-R is Parrinello-Rahman? 10 ns equilibration ends without any signs of
>> problems with the 1 fs timestep.  I then took the gro file from that
>> equilibration and re-equilibrated for 10 ns using P-R.  Did not last more
>> than 5 ns each time.  System is stable with Berendsen using a 2 fs
>> time-step.
>>
>> "It's normal to use tau-p around a factor of 10 larger for P-R than
>> Berendsen. They work in fundamentally different ways.
>>
>> I would also check whether your non-bonded scheme is consistent with
>> general practice for that forcefield in GROMACS (it may be, I just don't
>> know)."
>>
>> Thank you :)
>>
>>
> At minimum, your use of rvdw = 1.0 is incorrect.  It should be 1.4.  This
> could be related to instability of systems dominated by vdW interactions.
>
> -Justin
>
>
> I guess my question is then, should my system be crashing using P-R with a
>> 2 fs timestep and tau_p being 2 ps.  Increasing to 6 ps and leaving the
>> time-step constant at 2 ps seems to fix the problem.
>>
>> Cheers,
>>
>> Billy
>>
>>
>>
>>
>>
>> On 12 June 2017 at 20:05, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>
>> Hi,
>>>
>>> On Mon, Jun 12, 2017 at 11:21 AM Billy Williams-Noonan <
>>> billy.williams-noonan at monash.edu> wrote:
>>>
>>> Hi Experts,
>>>>
>>>> When running a simulation of cyclohexane in a periodic cell (constructed
>>>> such that the density is 0.779 g/mL) the simulation crashes during the
>>>> final 10 ns equilibration phase using Parrinello-Rahman as the barostat.
>>>> Changing the time-step to 1 fs fixes this problem.  Using a Berendsen
>>>>
>>> does
>>>
>>>> not lead to this issue.  Additionally, increasing tau_p to 6 ps with the
>>>> Parrinello-Rahman barostat, also fixes this problem.
>>>>
>>>>
>>> Looks like some of the integration setups are more stable than others.
>>> What
>>> is the volume doing during these runs? What does P-R 2fs do after a stage
>>> of P-R 1fs?
>>>
>>>
>>> I'm leaning toward the final solution, but I am wondering if this is a
>>>> reasonable thing to do.  I have read the Gromacs manual describing the
>>>> mathematics behind the Parrinello-Rahman barostat, and I have read the
>>>>
>>> mdp
>>>
>>>> settings page for Gromacs.
>>>>
>>>> It is still unclear to me whether increasing tau_p would affect the
>>>> simulation negatively at all, especially since it had been
>>>>
>>> pre-equilibrated
>>>
>>>> with Berendsen (2 fs time-step) and Parrinello-Rahman (1 fs) for 10 ns
>>>> in
>>>> separate runs before this run (tau_p is 6).
>>>>
>>>> Any advice would be appreciated :)
>>>>
>>>>
>>> It's normal to use tau-p around a factor of 10 larger for P-R than
>>> Berendsen. They work in fundamentally different ways.
>>>
>>> I would also check whether your non-bonded scheme is consistent with
>>> general practice for that forcefield in GROMACS (it may be, I just don't
>>> know).
>>>
>>> Mark
>>>
>>> Many Thanks,
>>>
>>>>
>>>> Billy
>>>>
>>>> --
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>>>>
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>>
> --
> ==================================================
>
> 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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-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

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