[gmx-users] temperature problem

[Lovika Moudgil]

Hi ..

Can anybody tell me about *nrdf* (*radial distribution functions*) value
that is in log file ..... How it effect our system !! Any link that I can
follow to understand its role more clearly !!!


Thanks and Regards
Lovika

On Wed, Jun 17, 2015 at 10:54 AM, Lovika Moudgil <lovikamoudgil at gmail.com>
wrote:

> 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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>>>> Gromacs Users mailing list
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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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