[gmx-users] Minimisation

Mon May 22 23:02:27 CEST 2017

On 5/22/17 4:59 PM, Pandya, Akash wrote:
> Sorry I meant 20 A. But I'll look into expanding the box size and see if it works. Thanks for your help.
>

Making the box larger is unlikely to be useful.  You should simplify the system 
by simulating individual components as the link I provided before describes.  A 
2-A box would clearly cause clashes.  A 20-A box should not, but you should be 
mindful of cutoffs and the requirement of satisfying the minimum image convention.

-Justin

> Akash
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
> Sent: 22 May 2017 21:52
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Minimisation
>
>
>
> On 5/22/17 4:42 PM, Pandya, Akash wrote:
>> Is there a chance that as my simulation box is quite small 2 angstroms and citrate is a charged anion, this could be a cause of my system blowing up?
>>
>
> I don't see how any sensible system can be that small.  Are you sure it's 2 A and not 2 nm?  Even 2 nm is too small given conventional cutoffs for most force fields, and you will always have an absurdly high concentration of any species in such a box.
>
> -Justin
>
>> -----Original Message-----
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf
>> Of Justin Lemkul
>> Sent: 22 May 2017 13:26
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Minimisation
>>
>>
>>
>> On 5/22/17 7:25 AM, Pandya, Akash wrote:
>>> What could be wrong with the topology could you please elaborate? I added glycine and citrate molecules  to the simulation box randomly. Could it be the fact I added topology for glycine and citrate in the wrong way?
>>>
>>> This is how my topol.top file looks:
>>>
>>> ; Include Citrate Topology
>>> #include "Citrate.itp"
>>> #ifdef POSRES
>>> #include "Citrate_posre.itp"
>>> #endif
>>>
>>> ; Include GLY Topology
>>> #include "GLY.itp"
>>> #ifdef POSRES
>>> #include "GLY_posre.itp"
>>> #endif
>>>
>>> [ moleculetype ]
>>> ; Name            nrexcl
>>> Protein_chain_H     3
>>>
>>
>> A series of #include statements is not a useful diagnostic.  You should start by inspecting your coordinates, particularly whatever atom 6640 is, and its surroundings.  There may simply be a bad clash there that can be resolved easily.  Otherwise, follow http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>>   Glycine should come from the force field itself and likely is not topologically problematic, but if you constructed your own citrate parameters, you should check their correctness, as well.
>>
>> -Justin
>>
>>> Akash
>>>
>>> -----Original Message-----
>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>>> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf
>>> Of Justin Lemkul
>>> Sent: 22 May 2017 12:13
>>> To: gmx-users at gromacs.org
>>> Subject: Re: [gmx-users] Minimisation
>>>
>>>
>>>
>>> On 5/22/17 6:47 AM, Pandya, Akash wrote:
>>>> Hi all,
>>>>
>>>>
>>>> During Minimisation I get the following output that the simulation ended prematurely.
>>>>
>>>>
>>>>
>>>> Steepest Descents:
>>>>    Tolerance (Fmax)   =  1.00000e+03
>>>>    Number of steps    =       500000
>>>> Step=    0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax=         inf, atom= 6640
>>>> Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax=         inf, atom= 6640
>>>>
>>>> Energy minimization has stopped, but the forces have not converged
>>>> to the requested precision Fmax < 1000 (which may not be possible for your system).
>>>> It stopped because the algorithm tried to make a new step whose size
>>>> was too small, or there was no change in the energy since last step.
>>>> Either way, we regard the minimization as converged to within the
>>>> available machine precision, given your starting configuration and EM parameters.
>>>>
>>>> Double precision normally gives you higher accuracy, but this is
>>>> often not needed for preparing to run molecular dynamics.
>>>> You might need to increase your constraint accuracy, or turn off
>>>> constraints altogether (set constraints = none in mdp file)
>>>>
>>>> How do I increase my constraint accuracy? Which file do I have to change?
>>>>
>>>
>>> That's not your problem.  You have infinite force, which means you have some catastrophic problem with either your coordinates or topology.
>>>
>>> -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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>>
>> --
>> ==================================================
>>
>> 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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>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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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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> 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
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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

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