<div dir="ltr">Hi,<div><br></div><div>Please ask questions related to GROMACS use on the users mailing list. This channel is for code development.</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Oct 14, 2015 at 2:05 PM toannt <<a href="mailto:toannt@vnu.edu.vn">toannt@vnu.edu.vn</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
Thanks. I'm defining two molecules types, each type have only one<br>
molecule in the simulation. When I said custom bonds, I was referring to<br>
the hydrogen bonds between the two strands. I'd like to understand how<br>
these bonds are handled by Gromacs in an atomistic simulation? If I have<br>
two strands at some distance apart, do they naturally come to each other<br>
to form the dsDNA?<br>
<br>
By the way, I am doing a grand canonical simulation, but I'd like to<br>
reuse libgromacs to avoid reinventing the wheel with some functions.<br>
<br>
Toan<br>
<br>
Vào ngày 14-10-2015 17:56, Berk Hess viết:<br>
> Hi,<br>
><br>
> There is no direct link between "real" molecules and molecule types.<br>
> The only restriction is that you can only define chemical bonds<br>
> between atoms within the same molecule type. Thus you can have two<br>
> DNA<br>
> strands in one or in two separate molecule types.<br>
> I don't understand what custom-bonds you are referring to. Usually<br>
> DNA strands are not chemically bonded to each other.<br>
><br>
> Cheers,<br>
><br>
> Berk<br>
><br>
> On 10/14/2015 11:49 AM, toannt wrote:<br>
>><br>
>> Hi all<br>
>><br>
>> I've just started to look at libgromacs for a custom simulation. I'm<br>
>> studying the gmx data structures to initialize them directly. I wonder<br>
>> if molecules such as DNA is considered by gromacs to be two molecule<br>
>> types (one for each strand) or is only one molecule type with some<br>
>> custom-bonds between the two strands?<br>
>><br>
>> Thanks<br>
>><br>
>> Toan<br>
--<br>
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