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

[Justin Lemkul]

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
>>>
>>> --
>>> 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
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
> 
> 
> 

-- 
==================================================

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

==================================================