Hello Sir,<br><br> Thanks for your reply sir. I will check to it. <br><br>With regards<br>M. Kavyashree<br><br><div class="gmail_quote">On Mon, May 30, 2011 at 4:59 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi Kavya,<br>
<br>
There is no way to correct for such things afterwards. But I would<br>
guess it's not much of a problem in your case. If a situation with a<br>
short distance is only transient, it is unlikely to affect the<br>
simulation. On the other hand, you may have secondary, indirect<br>
effects due to water ordering. Whether that is problematic in your<br>
case is something you'll have to assess yourself.<br>
<br>
Cheers,<br>
<font color="#888888"><br>
Tsjerk<br>
</font><div><div></div><div class="h5"><br>
On Mon, May 30, 2011 at 12:24 PM, Kavyashree M <<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>> wrote:<br>
> Hello Sir,<br>
><br>
> The difference between the rcolumb (1.4nm) and minimum image distance<br>
> that was obtained between two hydrogen HZ2 and HZ3 atoms of 2 lysine<br>
> residues (1.39714nm) is 0.00286nm = 0.0286Ang,<br>
> Since this distance is smaller than bond distance between hydrogen and<br>
> nitrogen which is ~1.0Ang, So will this effect the results of the<br>
> simulations?<br>
> Kindly let me know whether I need to redo the simulation again? or is there<br>
> any way to correct this or can it be ignored?<br>
><br>
> Thanking you<br>
> With regards<br>
> M. Kavyashree<br>
><br>
><br>
> On Mon, May 30, 2011 at 10:36 AM, Kavyashree M <<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>> wrote:<br>
>><br>
>> Hello sir,<br>
>><br>
>> I had used a dodecahedron cell for simulation. I have run<br>
>> the simulation for 100ns, did you man I have to restart the<br>
>> simulation again?<br>
>><br>
>> Thanking you<br>
>> Kavya<br>
>><br>
>> On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
>> wrote:<br>
>>><br>
>>> Hi Kavya,<br>
>>><br>
>>> > "shortest periodic distance is 1.39714 (nm) at time 21824 (ps),<br>
>>> > between atoms 2062 and 3688"<br>
>>> > where 2062 is a protein atom and 21824 is a water molecule.<br>
>>><br>
>>> 21824 is the time in ps at which the two atoms indicated, 2062 and<br>
>>> 3688, are at the short distance given. You can dump the frame with<br>
>>> trjconv and have a look. Probably your molecule stretched, or you<br>
>>> solvated in a rectangular box and the protein rotated. In the first<br>
>>> case, set a larger distance, in the second, use a rhombic<br>
>>> dodecahedron.<br>
>>><br>
>>> Cheers,<br>
>>><br>
>>> Tsjerk<br>
>>><br>
>>><br>
>>> --<br>
>>> Tsjerk A. Wassenaar, Ph.D.<br>
>>><br>
>>> post-doctoral researcher<br>
>>> Molecular Dynamics Group<br>
>>> * Groningen Institute for Biomolecular Research and Biotechnology<br>
>>> * Zernike Institute for Advanced Materials<br>
>>> University of Groningen<br>
>>> The Netherlands<br>
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</div></div>--<br>
<div><div></div><div class="h5">Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
--<br>
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