From: Morteza Jalalvand (jalalvand.m_at_gmail.com)
Date: Sun Jan 03 2016 - 11:24:45 CST

OK. Thank you so much.

On Sun, Jan 3, 2016 at 8:47 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
>
> On Sun, Jan 3, 2016 at 11:53 AM, Morteza Jalalvand <jalalvand.m_at_gmail.com>
> wrote:
>
>> Dear developers,
>>
>> In mergemols and selections2mol procedures (in topoutils.tcl), the box of
>> the new molecule is considered to be the largest of the available of boxes
>> (ie by setting a, b, and c to max of each molecule's a, b, and c) which is
>> necessary but not sufficient. If two molecules have the same a, b, c but
>> one of them is displaced relative to the other the box found by these
>> procedures can't contain both of them.
>>
>> This could cause problems in writelammpsdata procedure of topolammps.tcl
>> where cell dimensions found by min/max search are overridden by this
>> incorrect box.
>>
>
> ​true, but this is the result of a limitation in VMD​, which does not
> store the origin of a box, but only its dimensions. so for topotools it is
> not possible to know whether atoms are outside of a box due to PBC
> unwrapping or displacement of the entire box. it assumed the former, as
> that is the more common case when writing out LAMMPS data files.
>
> the only thing that could be done in topotools would be to never set the
> box dimensions after those merge operations, but that would be inconvenient
> in case the two merged systems share the same origin.
>
> in short, the basic rule "never trust automated procedures" applies. thus
> in your case, you should manually (or via script) determine what is a
> reasonable choice for the box dimensions and reset it to those parameters
> before writing out the topology and geometry to a LAMMPS data file. since
> you do know what operations you perform, you know what the box is supposed
> to be and that is much better than having topotools guess for you.
>
> axel.
>
>
>
>>
>> Regards, Morteza
>>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>