[gmx-users] temperature problem

[Lovika Moudgil]

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 ????


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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