[gmx-users] Ions drifting

[jani vinod]

Dear Justin,
Thanks for reply
I am using following attached mdp file
In raw trajectory protein molecule appears to be broken but ions around it
. So I processed the trajectory with trjconv whole option  followed by
nojump.
After that the protein appear on one side and ions on other

Thanks
Vinod



On Tue, Dec 16, 2014 at 6:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 12/16/14 1:34 AM, jani vinod wrote:
>
>> Dear All,
>> I am trying to carry out simulation of protein at 0.5 mM concentration of
>> NaCl.
>> It has been observed that within few nanosecond ions begin to drift in one
>> direction and protein in other direction. I am using Amberff03 force
>> filed.
>> What may the reason for the same.
>>
>>
> No idea unless you show us your .mdp file and any commands you're giving.
> Is this drift observed in the raw trajectory, or in something you've
> manipulated with trjconv?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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