[gmx-users] temperature problem

[Justin Lemkul]

On 6/6/15 2:03 AM, Lovika Moudgil wrote:
> Hi Justin ... Thanks for being so supportive . I tried things as you said
> and figured out that my slab is having problem with water .  I have one
> more question ... As I am working with golp ff parameters .. and it's
> parameters are fine for water . Like if I put one water molecule on my slab
> ..and run my system ...Its doing well ...but if I do same things with box
> full of water ... its not working !!! Is this possible?? Could it be
> because of parameters compatibility Or could be because of  my slab ????
>

Could be either.  Maybe the definition of the water-slab parameters is wrong, 
such that one water only infrequently interacts and the crash is rare, whereas 
with a full box, the bad interaction comes up frequently.  But at least it 
sounds like you've identified the problem.  Now the issue is how to properly 
implement the GOLP parameters; if you did this yourself, check your work 
carefully.  If you got the parameters from somewhere else, ask the person who 
created the files.

-Justin

>
> Thanks and Regards
> Lovika
>
> On Fri, Jun 5, 2015 at 10:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/5/15 8:09 AM, Lovika Moudgil wrote:
>>
>>> Hi Justin... Yes I agree my system is behaving absurdly . But I am
>>> wondering why !!I have done minimization without any error ..here is the
>>> result ...
>>> Steepest Descents converged to Fmax < 1000 in 1004 steps
>>> Potential Energy  = -9.6667906e+05
>>> Maximum force     =  9.7920349e+02 on atom 796
>>> Norm of force     =  1.7943926e+01
>>> ... I have One gold slab ...with golp parameters ..and amino acid on it
>>> ...in box with water and Na , Cl ions ....Freezing is for gold  only....
>>>
>>
>> So simplify the system - remove the gold layer and see if the remainder
>> works, do a system of water + gold, etc.  Your system is more complex than
>> you're likely giving it credit for.  Break it down - be scientific!
>>
>>   System is not that big . And thing is temperature remain at the value
>>> (that
>>> is 300K)  for few time after some time it start behaving weird . If system
>>> is wrong why its working even for one step ??
>>>
>>>
>> Probably because the starting configuration is fine, but the trajectory
>> evolves in such a way that it produces unreasonable physics.  Freezing is a
>> pretty severe perturbation.  Investigate the validity of the force field.
>>
>> -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

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