[gmx-users] temperature problem

[Lovika Moudgil]

Thanks Justin ..... Your suggestions helped me a lot .... I got it !!!! .


Regards
Lovika

On Sun, Jun 7, 2015 at 7:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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> Gromacs Users mailing list
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