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

[Billy Williams-Noonan]

Also, the topology for the cyclohexane comes from the ATB and looks very
reasonable.

On 12 June 2017 at 20:25, Billy Williams-Noonan <
billy.williams-noonan at monash.edu> 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 :)
>
> 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
>> >
>> > --
>> > Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
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>
>
>
> --
> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
> <http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
> **|*   +61420 382 557 <+61%20420%20382%20557>
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
>
>


-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

*LinkedIn Profile
<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052